This happened to me every now and then until I got my top tier pet and it hasn't happened at all since then.
I had problems with my pet names resetting, for me the problem seemed to happen to pets that had the same name which would cause all but 1 to reset to default, overcame the problem by changing a few letters to upper case.
I'm having odd trouble with the names I assign my pets... they keep resetting, but they don't even do that in a predictable manner. I'm pretty new to MM'ing, so I'm posting ithere to see if it's a known issue, with or without a known workaround...
Somehow, the same second zombie that had been continously resetting to 'Zombie' was now resetting to 'Roma', which I'd futilely attempted to make him into BEFORE... guess the joke's on me. 
Basically, I'm a Necro MM with a Vampiric them, so I named my fist zombie 'Roma', after the undead servants mentioned in Bram Stoker's classic 'Dracula'. Good so far. Then I get a second zombie, and rename that one to Roma as well - it turns into Roma 1 and Roma 2, works for me. However... in the next mission, when I summon them, the second one has reset to the default 'Zombie' again. I changed it to Roma a couple of more times before giving up and leaving it as Zombie... figured it was just an issue with renaming them both to the same thing.
However, when I got my Grave Knight, I'd gotten a bit tired of those serious names, and I'd just bought a Marx Brothers DVD, so just for laughs, I changed the names of my three minions to 'Harpo', 'Chico' and 'Groucho'. Good for a laugh... but next time I summoned them, guess what I was stuck with?
Wrong!
It was Harpo, Roma, and Groucho.
So, sound familiar in any way?