Not sure what the bigger problem is (the timing stuff... sorry) but there isn't actually a way to "Turn Off" lanes. Only hide them.
Anything thing done to the "parent" track with lanes closed is pretty much guaranteed to cause a chaotic mess in the hidden lanes unless there is only one clip/take hidden.
The relationship between the parent track and lanes is a bit of a contentious one with me (and I have suggested improvements in the past) but all in all there ain't much that can be logically done to fix such things because the Parent track is merely a summation of the take lanes. If you try to edit the parent track without consideration to the lanes that are hidden bad things happen.
This is why whenever I'm tracking/editing/etc in a specific track I keep the Lanes open to keep an eye on what's doing what then use the Flatten or Bounce features to get my desired final track together, move it to a blank track and THEN I can safely screw with it in the Parent track.
I honestly think we need some kind of added edit "mode" for more old school type workflows where the Parent track responds more like tracks used to before Layers and Lanes.
For now though the Comping/Lanes stuff is pretty cool and useful (I actually love 'em) but they really are jarring and quite different than just being able to edit what you see in the tracks (which are just an image/composition of the hidden lanes and depending on the Record/Edit modes will do some CRAZY unwanted crap when trying to edit like in older DAWs).
Once MIDI and SS clips start getting involved? Oh crap... it gets even nuttier. However a simple bounce of composite performances/edits/whatever so it's all one long MIDI clip can help.
Meh... I'm probably not really helping but this is most likely related to new features getting in your way.
Otherwise maybe it is some kind of SS or Snap bug I'm not aware of.
I don't use SS often and if I do I convert to standard MIDI clip rather quickly.
CHeers.