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I had the same problem and when I went to the developers web site he was talking about how when it is included with the new ROM it gets put in a different folder and then you can't update it or download it from the Market. I just tried uninstalling it through Applications>Manage Apps> SetCPU>uninstall and then redownloaded it through the Market and it worked fine, even got the newest version 2.X It's actually very different than the 1.6.x that I had running after installing SS 4.4 ROM. Give it a try, maybe it will work for you
Has anyone been complaining about problems when they move apps to the SD card? I have never had as many issues upgrading one of your ROMs until 4.4 The only difference I could think of is that I had moved a lot of my apps to the SD Card to free up memory. I wiped 5-10 times, re installed several times and it wasn't until I moved all the apps back to the phone, wiped 4 times, re-installed the ROM and changed to Apps to SD Off that the phone is running solid. Before, I had FC's Phone Locks that needed a battery pull, etc... Even changing kernels didn't help. Was there something funky with apps on the sd card in 4.3? Was something fixed in 4.4 for running the apps on the SD card? I ask because I'd really like to move as much to the sd card as possible but I don't want to run into this problem again. But I got to say, you've got by far the best ROMs around! I sent you a few beers just to show my appreciation.
Oh, and all of the apps I had on the sd card didn't restore with the rstapp -c command. I had to reinstall them using Titanium which is another reason why I thought there might have been an issue with apps on sd card in 4.3 since that is where my backup came from.