If anyone wants to help me out with this, I'd appreciate it greatly.  Here's the background:

After a long time planning, I finally set up my custom storage server.  It's a box with several drives running a windows 2012 server.  After doing some tests and research, i settled on using the FLexraid Traid product, which is a drive pooling software raid system.  I initially tried the new windows storage spaces, but didn't like the speed and features.  Traid sold me on the fact that you can pull a drive out and the files and everything are intact without much fussing around at all.

OK, here's the problem.  I set up my first active directory domain services.  Then, unfortunately, I accidentally removed ALL the NTFS permissions from my main almost root folder.  This was bad and now I've lost access (access denied) on a lot of the folders on the storage array.  I've tried everything to reset the NTFS security and all that.  I tried all the tools out there.

Unfortunately, the developer of the software raid explicitly has said he will NOT spend a second helping people with NTFS security problems.  So I'm stuck on advice.  I've scoured the web and tried everything.

Some interesting facts:
--If I stop the storage array and just connect the drives individually, I can access all the files and folders.  I can also successfully modify the NTFS permissions with those tools mentioned.  When the array is active, however, I cannot access all the folders (access denied).  So that's why I'm confused.  The great thing about flexraid, the reason i got it, is because you can access the files in this manner.

My ideas:
--my first idea is to uninstall/reinstall active directory on the server.  or even reinstall the entire OS.  I have no idea if that will work, I guess I'm assuming if all the active directory details are reinstalled, maybe the files will think it's a new server and can start over?  i don't know.

--My other idea is to copy the contents of the drives to a temporary external drive, then copy them back over or something.  The problem with this is that I'm not sure i can delete the problem directories.  i don't want these broken directories forever on the server.

So I'll take any advice.  I don't think the files are damaged or anything.  Just the NTFS security.

I got into it a little with fodder in another thread.  So I wanted to continue this discussion specifically here.

I want to talk about the problems with USB 3.0 in any Windows OS (desktop or server).  If you haven't experienced problems with USB 3.0, you are not going to help the discussion.  In other words, I'd like to figure out a solution if it exists, or at least nail what the problem is.

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So, my experiences...
I've had several USB 3.0 experiences.  Some on desktops I've built myself.  I've used the more recent motherboard built-in features, I've used addon PCI cards, I've used expensive laptops that come with nice USB 3.0 features on them, including my Surface Pro.  The Windows OS's I've tried: Windows 7, Windows 8, Windows Server 2012 R2.

My goal (I guess) is to have an external enclosure where I can swap drives in and out, use them on several different computers, and not have problems.  I've never really had a nice experience in these terms.  I've had success in isolated cases: for example, and enclosure+drive works well on my laptop, no problem.  But I don't think I've had success with using an enclosure+drive on multiple pc's without issues along the way.

Scenario 1:
I have an enclsoure+drive that has esata and USB3.  I first tried USB3 on a Windows 7 desktop.  It didn't work very well in that sometimes the device was detected, and other times it was not.  And sometimes, when it did connect, a popup would immediately ask to format the disk.  Which I didn't want to because it had data on it and was working before that incident.  Usually when this happens, the drive is already corrupted.  This has happened several times.  Usually occurs when trying the drive on different USB ports, or on different computers.  And the reason to try it on different ports and computers is because the drive was not being detected on the first try.

Scenario 2:
After experiencing Scenario 1, I lost trust in the USB3 connection.  So I decided to use the available esata port.  I really have not had problems with esata, I like it a lot.  However, some computers don't have esata, so when I take the same enclosure to a computer that lacks esata, I use the USB connector.  Problems occur, similar to above.  Where the drive gets corrupted and eventually needs to be reformatted.  When this happens, I end up using the esata port on the computer that works, and I stop trying to use it on other pcs.  I don't like that, but at least it works.

Scenario 3:
In this case, I don't have esata, only USB3.  I plug it in a USB3 port, it's detected, and I start transferring files.  If I do a significant amount of transfers, let's say 100GB...I've very often encounter the drive disconnecting in the middle of the transfers.  This usually turns out to be a power issue, but it's not always clear.  I've had it happen with extra power, too.  Some enclosures can add extra power, others cannot.

Scenario 4:
This is the new one for me.  I got an enclosure that can RAID-0 two 2.5 drives, with USB3.  I love the idea for speed and portability.  So far, it has had some minor issues, not enough to really be a problem, but enough to make me nervous.  it worked with Windows 7, but initially had a hard time being detected consistently.  One of my drives was fresh, the other had stuff on it.  after formatting and fiddling around a bit, it worked.  It worked on Windows 8.1.  It didn't work on Server 2012.  It causes it to hang.  But the bigger issue is that after plugging it into Server 2012 machine, it didn't get detected, and the drives got corrupted and had to be reformatted on the other computers.

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So what's going on?  How do you get USB3 to work well and all the time?

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I'm going to list many of the common solutions for USB3 problems.  In my experiences, they don't do anything most of the time.  But these are the responses that are all over the internet.
--Disable the power/suspend settings for the USB hubs.  Nice idea, rarely fixes anything.
--Similarly, adjust the power settings in Windows.  This has worked occasionally, but doesn't appear to be the problem.
--Bad controller on the enclosure.  I think this is nonsense.  I've had drives being corrupted the same exact way on several completely different enclosures.
--Replace drivers or firmware.  Also does not seem to do anything.  And figuring out the driver or firmware that needs to be replaced is also somewhat impossible.

http://edgerunner.com/spacemonger

Spacemonger is now updated after a very long hiatus!  The economy must really be picking up or something.

I just have to say something, I personally feel Spacemonger is one of the most perfect softwares I have ever come across.  It is flawless, i really can't say that about maybe ANY other software.  The first time I saw it, i was blown away immediately.  It's simple, it's powerful, it's visually amazing, it's tremendously practical (like, I can't live without it).  It's like the Mozart of software.