I checked the files in the OP and they are all good. I will reflash myself tonight just to make sure. The only other thing i can think of is RZ Recovery might cause this bug during the flashing part. I use CWM and never had a problem. Just a guess though..
I have had this problem lately as well. Even wiping everything and rebooting into recovery again installing the three items, boot.....only 2.0 with the 2.1 upgrade notification. I tried RZR and CW recoveries with the same deal. I have successfully install it with your method before like a week ago too. My only thought is that some of the folders/files that Sourcery puts on the SD card on an install that are left over after a wipe are causing and issue?
Right now I'm just running a vanilla stock but rooted 2.2.2