Either way, it is a jarring incompatibility between the hosted and native AROS versions.
After some hassle I managed to compile newer AROS hosted version (deadwood's altabiv0).
Then I tried odyssey/owb 1.25 binaries. First it crashed because somewhere in update_prefs() it did not check whether program icon (diskobject) loading succeeded (0 access). Then it started and I found out how to reproduce instability. It turns out stack size for "[OWB] Timer" somehow was allowed to being too small (4096) (for AROS hosted where some stuff on Linux side uses Exec stacks too). Changed exec/NewCreateTaskA() to not allow stack sizes smaller than AROS_STACKSIZE.
Then quick tests seems to indicate it is no longer unstable.
Debugged with gdb.