Ok now I know l8ter is going to jump on me for saying this, but here goes.
I had a similar problem when I did a fresh restore on my iphone 4. Instead of manually entering the sources list I just transfered them over with cyder. All seemed to be going well, until I went to Sinful's repo to download an app. Got the size mismatch error. Ok I thought maybe just the app. Tried a different app, same result, I started trying all the apps and was getting the same result.
So what I did was drop a new cydia into the autoinstall folder, reboot. Manually added sources one by one and hey presto, the size mismatch error vanished......
Now I don't know if it was just a corrupt file (source or whatever) but it did fix my problem.
Anyway, the reality is though that most size mismatch errors are as l8ter points out. Mine was I was just trying something different to see if it would save time and I think I screwed up somewhere..... Never know though till you try