What is attached to your Primary IDE interface? Presumably a hard disc - if it is running in PIO mode you have a problem somewhere. Do you know what kind of drive is installed (make and model) ? If you don't know try running SIW
to find out.
I presume your Secondary IDE interface has a CD or DVD drive attached - in which case DMA Mode 2 is probably correct.
This article may help: http://support.microsoft.com/kb/817472
Try the workaround before you try the hotfixes. This has happened on my system before now and everything grinds to a halt. Using the workaround will help solve the problem.
You may also want to check your hard disc hasn't got bad sectors before that though. Disc errors are a common cause for IDE drives reverting to PIO mode.
Go to START > RUN > CMD.EXE
and for each of your hard drive partitions run: CHKDSK C: /X /R /V
each time replace C: with the drive letter.
For drive C: (and possibly others) it won't run because Windows can't release the drive while it is up and running. When prompted allow it to do a scan on next reboot.
When you have checked all the other drives reboot your system and allow the locked drives to be scanned too.
This check will do a complete surface scan of your hard discs (an if you have a large drive it will take some time). It will help identify any bad sectors on your hard discs and map them out so they won't be used in future. If files are currently using bad sectors it will attemt to recover the files and move them somewhere else. If it can't do that the files are salvaged into the root folder of the drive and given a name something like ******.CHK. Depending on what files are damaged it may account for why Windows isn't working properly and you may have to do a repair install of Windows to replace damaged system files.
Even though it takes a long time you may want to sit and watch as the boot time scans are done so you can see which if any files are having problems. Have a bit of paper hand to note them down.
If you need any more help post back again with what happened.