I used the Registry cleaner in CCleaner and when I rebooted, the Synaptics trackpad driver wouldn't run. So I reinstalled the driver and everything was ok, and I ran the registry cleaner in CCleaner again. After looking at what it was deleting, it was actually removing synaptics entries.
I have the same problem here, after running the registry cleaner Synaptic Touchpad Enhancements crashes immediately and every time it tries to relaunch after a reboot.
At first I didn't realize that it was CCleaner that had caused this problem but it has now happened to me twice forcing me to reinstall the touchpad drivers each time.
This time tough I reran CCleaner right after the driver reinstall and backed up all the Synaptic keys, I'll attach them to this message. I renamed the file to .txt instead of .reg though since I wasn't allowed to upload .reg files. Running this file after a registry clean in CCleaner fixes the problem again.
Hopefully these keys will be ignored in some future version of CCleaner. If the author of this otherwise very good program reads this message and needs more data or something to fix this issue I'll gladly help.
At last I'll add that I also run Windows Vista 64-bit but I don't know if we are the only ones with this issue.