You didn't mention your Cydia version; I will assume it is 1.0.3222-73. This is a long shot, but you might try installing the newer version of Cydia, 1.0.3366-1, to see if that helps. You can get it here:
http://apt.saurik.com/debs/cydia_1.0.3366-1_iphoneos-arm.deb
You would need to use SSH to put this on your iPhone, somewhere like /var/stash. Then you would navigate to the .deb file in iFile, tap it and select Installer from the menu.
The problem with cracked apps, aside from the piracy aspect, is that you would never really know what you are getting.
By the way, that "essential upgrade" was like a month ago wasn't it? And your Cydia apparently was working for a while after that. Did you install that Icy app? I tried that and found it was making the AppStore act funny and I had to get rid of it. I never saw a problem with Cydia, but maybe because I never actually installed much of anything with Icy.