With some of AMD's latest drivers, they implemented a function that will place the taskbar on only the center monitor, instead of having it stretch across all monitors. I have been having this same problem every time I switch back to an extended desktop (3 separate resolutions). Each time I have to check the auto-hide taskbar box, hit apply, then uncheck the auto-hide taskbar box, and hit ok.
Honestly I didn't mind it before these new drivers. In fact, with the new drivers, the function doesn't even work properly for me.The taskbar remains stretched across all 3 monitors in eyefinity, but I still have to deal with the auto-hide workaround every time I switch back.
As far as I know, we just have to wait for the next driver version to be released. What I don't like about this new driver is that ULPS cannot be disabled, meaning no overclocking past 1125 MHz, which bothers me somewhat because on the old drivers my reference 7970 barely had an increase in temperature even with a voltage increase from 1.17v to 1.25v (same fan curve on stock and OC clocks). This gpu is great for overclocking, so LET ME OVERCLOCK, AMD!!!