Despite some warnings in Komodo docs, I was running Eaccelerator and Xbedug extension at same time. I just thought I was lucky and could enjoy both. Well, the debugger was broken in subtle ways. Namely, it would skip ahead various lines when i *step into* a function. Step over worked fine, Step in didn't. So if you are having PHP debugger weirdness like that, disable the Eaccelerator and use APC or XCache. Both of those are compatible, in my testing.