Since you told this happened after updating to 3.6, I made some test with the new default theme Twenty Thirteen, coming with WP 3.6.
I don't know if you are using the Twenty Thirteen, but anyway please try to take the following tests:
1. Clone your actual Black Studio TinyMCE Widgets using the native WordPress Text Widget: for each visual widget you have, create a corresponding text widget and copy/paste the content from the HTML pane of the original one. Then disable Black Studio TinyMCE Widget plugin and check what happens. If the same issue occurs also with WP native text widgets, then it's definitely not caused by our plugin.