Well I know what the glitch is about, but not what caused it.
If you charge a jumpdrive with for example 100 000 charge, change the config so it actually needs less charge for that ship, then upload that in-game by pressing Tab + .
You get this issue. It's basically the result of getting your charge over the actual limit.
Now I'm not sure if this was caused by an admin uploading a changed config for jumpdrive/scanner which caused it to go negative, but most server owners do a restart for that.
Is it possible that 2nd thing happened for you?