Somehow I didn't find your posting before, but I have the same problem and I just posted a new question about it:
Hopefully we get some answers on this.
Hi, I'm experiencing the same issue. I believe this was since a recent update (Java or Adobe).
I still haven't found out a real solution, but I did find a workaround: if you just click on the address bar and select the address (gmail in this case), then you're able to switch windows again.
Hope this helps.