If you can make some process snapshots during any periods of freezing or find automatic snapshots from actual crashes, send them to us and we can often tell you what's causing it from those as well.
Tools which mess around with other program's windows are often confused by our progress dialogs, probably due to the number of threads involved or the way we handle z-order, so it's probably one of causing the problem, but the snapshots will hopefully reveal if that's the case or something else.
Problems launching executables could also be due to antivirus, and might be a separate issue (or could be the same underlying problem, too).