i've been modifying nonstep for months now .. so if theres anything i can help with ... :)

first i'd replace $ModulesDir$grdtray3.dll with $LitestepDir$systray2.dll ..
do not update to the latest layercuts.dll.. weird on-top-problems appeared when i did that
but i think the module with the most stability issues used in nonstep is grdtray

oh, and update your indiestep build too :)