A program (allowing me to zoom with my trackpad) ran at startup on my computer. Then I disabled it through Administrative Tools > System Configuration > Startup. When I re-enabled it that same way it would not run at startup anymore. In the list it was the only program using %ProgramFiles% instead of C:\Program Files\ so I changed it in the registry HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run. Then it started correctly. It was strange though because the %ProgramFiles% path (when I put quotes around the whole thing) worked from the command line.
It's also strange that about half of the programs have quotes and half of them don't, but it does not seem to stop them from starting.