I have the sam problem in AI where all the sudden my hotkeys don't work, and I use them all the time. In fact I rarely use the toolbars.
I have problems when I save as a PDF, where if I transfer it onto a windows network, the file won't work. And I've tried all the different options, and done the extensions correctly. The same thing happens with jgs.
Also, when I save as a pdf I often get "error -42 cannot be be created, illustrator is having difficulites". So I have to revert to 8 and save the pdf.