It could be a couple of things.
1. Perhaps you have not completely removed the infection. Instructions for it's removal can be found
HERE.
2. You have completely removed the infection and parts of Windows are broken from it's removal. This is not unusual, but I would not attempt a repair at this point until you have completed ALL of the steps in the removal link above, and then come back into this forum and we can help you get the computer back to normal.