I have seen the "storyboard going funky" as you described:-
It only happens only when the project becomes complex (not sure exactly how complex)
It can be triggered by setting RTMs or by adding music soundtracks under the menus (there may be other triggers too but those are the two that bite me)
In my case the "funkiness" appears to be harmless - affecting the storyboard (and, to a lesser extent, the timeline) display only; I can switch to timeline view and carrry on working (the only thing I see wrong there is that the menu numbers get changed and are no longer in a nice progression adding 1 each time (so for example you might see M1, M2, M4, M6, M7, M11 instead of y#the nice sequence of M1. M2, M3, M4, M5, M6 above the menus.
The problem goes away (temporarily) by saving and reloading the project, and can sometimes go away as a result of making an edit.
To minimise confusion when making a complex project I will add all of the clips and menus and set all of the chapter and inter-menu links, then the very last things I do are to add the background music to the menus and set the RTMs.
Regards,
Richard