I'm now at the point of thinking this is not .NET related...
I would also suspect it isn't. Whatever the other issue is that seems to stop PE6 starting, this appears to only affect opening and saving, file access.
The only times I have had long pauses, often very long pauses, and not just with PE6, is when Windows remembers I have used a networked or shared drive, or some removable device, and it is twiddling its thumbs while waiting to see if it can find that device when it can't, and isn't going to.
Windows seems to track opens and saves separately, and may these days be even more fine-grained than that, so one thing may work but another then hangs for ages. Windows also seems to remember what happened in other apps so a delay in PE6 may not be a result of anything done within PE6.
One of the problems is that, once it gets into this pausing, it can be hard to kick it out of it. Opening or saving files in various places will usually have the 'no longer exists' drop off it's most recently used lists.
There can also be long delays when Bluetooth devices have been used, which present themselves as 'we might be here, ask us, and we'll spend ages shouting into the ether to see if what was there is still there before we let you know it isn't' though that shouldn't affect file opens and saves.
The only thing I can suggest is to try an Open, let it hang, show "Not Responding". Don't click elsewhere within PE6 other than keep clicking wait prompts, and seeing if it does eventually offer up the Open dialogue which is expected. You probably don't have to sit and wait for each pop-up, as it's probably still looking in the background. It's perhaps one of those things to try in an evening so you can click as you pass it, leave it be, until you think it's time to throw in the towel.