Sorry - didn't browse this whole thread but I hope that this will answer some problems others out there may have.

I had installed glTron, nehegles and some Python Qt stuff earlier to my N900. I tried to update and device told me to use USB which was not what I wanted - update would be enough instead of "clean install".

Here's what I did:

1. (took backup here - never hurts to take one)
2. rootsh apt-get remove nehegles
3. rootsh apt-get remove gltron
4. rootsh apt-get remove libgles1-sgx-img
5. rootsh apt-get remove libqt4-test

After these "clashing packages" were removed (with possible dependencies) installation via SW manager update was possible and a success.

Really hope that this helps