Try this from the C:\Windows prompt you mentioned:
1. cd C:\Program Files\jv16 PowerTools 2009\Backups\_StartupManager
2. dir
3. cd C:\Program Files\jv16 PowerTools 2009\Backups\_StartupManager\000FE3
4. dir
5. regedit Entries.reg
Guidance:
1. Assumes PT is installed at C:\Program Files\jv16 PowerTools 2009
2. The command should list one subdirectory for each startup task you disabled; the names have 6 alphanumeric characters; write them down
3. Substitute one of your subdirectory names for 000FE3
4. Optional; it just lists the files in the subdirectory
5. Restores a startup task that you disabled
Repeat 3 through 5 for each subdirectory name.
To confirm, I actually did 1 through 5 successfully from a C:\ prompt on my Vista desktop.
I hope it works with your windows CD C:\ prompt.
Note: all this assumes the tasks you disabled originally started from the registry. If some started from somewhere in the file system, their recovery from a C:\ prompt would be more complex, but still possible.