I have installed a new version of WP 4.1 and can reproduce this bug without any other plugins installed or activated. There is one sidebar (the one from Twenty Fifteen).
The bug occurs, if there is more than one TinyMCE-Widet in the sidebar. In my test-case there two widgets. the first one works fine and the tooltip is perfectly aligned. the second one with the same content has a misaligned tooltip.
I hope this helps. Jonas