I think I had a similar experience...
When I tried my second beta of Mozilla (Win32 I think), no window would appear on launching the app. I couldn't figure out what the problem was. I think Peter said it had something to do with .ini files or something. Bottom line - Mozilla knew where the old version was and was trying to use something built from it during the installation/first startup automatically (bookmarks or something).
I assume the OS/2 version also looked for the old directory during the install (even if nothing was installed there).
I'd suggest .zipping up your old Mozilla installation, cleaning out the relevant .INI settings (if any) using INIMAINT or similar making sure all obvious remnants are gone, and reinstalling the latest OS/2 Mozilla beta you feel comfortable with (maybe a nightly, maybe not). If that still crashes your system, then something's clearly amiss (maybe the old bugaboo of video drivers) and I guess you'll have to go back to an earlier build.
HTH a bit. Good luck.
Cheers,
Scott.