glad to hear we've found the nature of the problem!
no need to apologize, it wasn't stupidity, its something people have encountered before.
however there is something important you need to check and make sure you got right.
you found the "c:\users\...\documents\DonationCoder\FindAndRunRobot\AliasGroups\MyCustom" folder -- and THAT is where your custom aliases should be when you are using the install version.
So, this is what I did to solve the problem:
* I grabbed the portable zip file
* unzipped it in my FARR directory and
this may be problematic and you probably don't want to do this.
by doing that you are telling FARR to try to save all of its files inside that directory -- which windows will not like!
if you are using Windows XP then it's ok and you don't have to worry -- but if you are using a new version of windows, it may behave ok but you might have problems with your custom files being saved later by microsoft windows in weird places (virtual shadow directories -- you don't want to know!).
So.. Here is the better solution:
Delete the ConfigDir.ini file in the C:\Program Filesx86\FindAndRunRobot\ directory
Now that you have done this, FARR will behave normally and will try to load your custom alias files from "c:\users\...\documents\DonationCoder\FindAndRunRobot\AliasGroups\MyCustom" and try to load your settings from your c:\users\...\documents\DonationCoder\FindAndRunRobot\" directory, which is what you want on windows vista,7,8, etc.
Then you may need to copy your old good MyCustom directory from your previous portable install into "c:\users\...\documents\DonationCoder\FindAndRunRobot\AliasGroups"
Does that make sense?
To summarize, your goal is to have your custom settings in your "c:\users\...\documents\DonationCoder\FindAndRunRobot" directory.
To be really sure, you might want to start over by deleting your C:\Program Filesx86\FindAndRunRobot and then reinstall FARR from setup program, and then copy your custom files from the old portable install to "c:\users\...\documents\DonationCoder\FindAndRunRobot\" that would help you be sure that it's loading the files from the right place.