I'm still testing this one but it is reproducable (at least on SMP):

Step 1:

1. Create a reactor with a redstone port
2. Set the redstone port to be turned on/off from signal
3. Enable redstone signal to turn reactor on
4. Restart server while both redstone signal and reactor is on
5. Remove redstone signal

End result:

Reactor no longer honours the redstone signal setting, it will remain on even when the signal is no longer being transmitted (in my test case it was using redstone conduits from enderio).

Reactor remains permanently on and cannot be shutdown from control panel. Only fix is to either break and replace reactor or change the redstone port to another setting at which point everything goes back to normal.

Interesting. Does this reproduce only with EnderIO conduit, or with vanilla redstone as well?

I'm not able to reproduce this with vanilla redstone or RedNet. I'm inclined to say it's an issue with EnderIO's particular version of Redstone conduits.