Hey ivan,
...That sort of ini problem generally appears when the ini files become over full with crud (where programs write to the ini files but don't clean up after themselves).
When was the last time you ran an ini cleaner like Cleanini or Checkini from wptools or Xfix included in Xworkplace? Depending on what you are doing you may need to run of then once a week.
Well, I am rather religious about running clenini, last time was literally just 2 days ago. I pretty much try to do it once a week, the goal being a clean report-out, which I always get (so no left-over corrupt objects, etc, etc).
In my particular case I find that a re-boot within 1 day of system boot usually gives me a clean 'save', anything beyond that usually ends up giving me a corrupted 'save', so that I pretty much know upon re-boot my WPS will be corrupted. In such situations the OS2SYS.INI file is alway chopped down to about 600k from the normal size of about 900k.
I can only guess that this is a symptom of memory contention in OS/2. Almost like clockwork, if I end up running FF for an extended amount of time, to the point where the available memory on my 4Gig box drops down to <1Gig, then the shutdown will produce a corrupt OS2SYS.INI file.
XFIX has been of use before, I normally run CHECKINI.