win 7 SP2; AI CS6.
Upon saving, usually there is a progress box in the middle of the screen. It appears after the save begins. Usually the box shows the progress is about half way along, and shortly, it gets to the end, then after a few moments, it eventually disappears and all is saved. However, occasionally, the toolboxes turn black and even flash during the saving process!
It's very strange. I have dual monitors on the computer; the left monitor is for the main application and the right is where I keep all the tool panels, mainly layers, appearance, glyphs, navigator/info, transparency, character/paragraph/opentype, document info/attributes, brushes, graphic styles, gradient and stroke with appearance. I have the UI set to light grey to work with.