Do the problems still occur with recent PekWM versions (from git)?
Yes, Xinerama is enabled for both X and pekwm. As I've said, it does work for all apps I use except mozilla based apps and Konqueror.
Another observation which probably is related: When I have a workspace with only a window of one of those "bad apps" and close that, then I cannot switch to another workspace with Mod4-<number>. Switching with an external pager application works, though. Should I submit a new bug report for it or is this remark sufficient.
I've experienced this with Firefox and it actually seems to be Firefox being confused and not pekwm. This happens with Metacity as well. Maybe we can work around it somehow?
Do you have xinerama in both X and pekwm enabled?