You can't, it's supposed to do the compacting every 100 times the program has been opened. Let it do it. It is routine maintenance built into the program. All it does is 'tidy up the file system' - a bit like defragging.
It normally "pops up" as you close Outlook Express (for the 100th time) - so shouldn't interrupt anything. As mfletch says you need to let it do it. It should only take less than a minute to complete. I've known "messing with the registry" to change the counter cause even more problems.