I have scanned all of the files included with Start++, including the installer itself, for viruses before uploading them and never encountered any problems. I did encounter a false positive against the "runnonadmin.exe" component a couple of days ago from eTrust (CA anti-virus) and they are looking into that. Apparently they are setting off false positives against a lot of executables with their latest update.
However, this spyware notification is news to me. I wonder if they're flagging anything that uses windows hooks? Start++ does not record any keystrokes, but it does redirect them when you are typing into the start menu (so that it knows whether you've typed a shortcut that it needs to handle and such). It's possible this is setting off a false alarm in Spyware Doctor. I'll make a note to look at that product and see if they have any workarounds or exception processes that I can look into.
The keyboard hook that Start++ uses is only installed while the start menu is visible - does Spyware Doctor flag the program when it starts? Or only after you've opened the start menu? (I'm just curious about how exactly they even know what Start++ is doing).