While I was penting, I had summoned a GC and left it to fight some grolms. I'm not exactly sure what happened to it after some time, it probably died, but suddenly I noticed with the "/who" command that the Red Back NPC was flagged as my GC.
Since I had /gctome active, Red Back himself followed me to the temple when I recalled, where the guards proceeded to swiftly smack him into non-being.

hm...

Not even sure how that could happen without it always happening.

GC dies.
Redback respawns and uses your old GC's id - before your GC id gets deleted off you.

Very strange.

I could put in a trap for that but I would like to know the cause rather than covering it up.

Happened again while penting today. It would seem that the GC suddenly ceases to be for some reason, and I don't think it's getting killed by enemies (there wasn't any 'GC died abandoned, lost luck' message).
After penting for a bit, I typed '/who' to check if the GC was still around, but there was just me, which seemed weird since I wasn't informed of its demise. A bit later, I checked '/who' just to make sure, and apparently a grolm had taken its place.

When I recalled, the grolm followed me to temple as per usual; tried some GC commands on it to no avail, guess those are exclusive to the actual minion. Guards dined grolm that night.

[quote]

Very curious.

I would guess this problem has existed since the beginning of time.
The case of the lost GCs whenever the GC template got reset.
It has only come to light with the arrival of the /gctome command.

Today when I logged in, I had a spellcaster from lab3 as my GC (only noticed when using sewers entrance). Curiously, checking /who it also had the ID 5014.
I don't remember the mechanism that links a GC char to its master char, but the first GC I summoned probably glitched/vanished somehow and I remained associated to whichever char had its ID, 5014 in this case.
I summoned a new GC and immediately transferred it, for all I know this temporarily fixes it? Will report any more strange behavior that might happen.

Ancient bug squashed.

Well done on the reporting.
It was the screen shot with the GC ID that gave it away.