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