I think I found a solution! I struggled with that for ages but I almost ignored this issue up to this point when I got extremely annoyed as my workflow slowed down… Well simple solution: if you “bounce in place” then click okay when Cubase asks you to replace current events it seems that everything is in sync again and the strange free warp tool behaviour is gone! Let me know if it only fixed that for me or you found that it worked for you too! 
Hi everybody,
I’m encountering the same problems (C11 pro): I have a tempo track activated and when I edit in the sample editor all edits appears to be moved left… No toggle musical/linear time base, no disativating time warp tool, no bounce in place and replace are solving the issue…
Any new idea?
Thanx,
Art
Hi, same problem here. Using C10.5 . But happy to report that I’ve seemed to fix it by using the prior mentioned Time-Warp workaround. Actually, after creating my 1st “warp marker” then dragging it around a bit, then undoing it, then going back to the selection tool… it did not seem to work. But after I created more “warp markers” then dragging them around a little bit, then undoing, then going back to the selection tool, then closing the Sample Editor, then going straight back into the Sample Editor (…I think I went back straight into it…), THEN the problem was/seems fixed…! 8·D … Gonna test some more…
ps: …have to say i’m glad i didn’t upgrade Cubase… but only if it’s true that this workaround doesn’t work on more recent upgrades…