Yes, that's brain-bendy.
He should earn time XP at ECL 4, as that's definitely what should happen if had no choice but to remain a wererat. That gives him a total of 4436 XP.
If he retains his lycanthropy, then he needs to reach 10,000 XP to gain another class level.
If he is cured, then he reverts to ECL 1 but with "too many" XP, so I think he has no choice but to level up once and then lose the excess XP, giving him a new total of 2999 XP, one short of 3rd level.
If he had managed to avoid the wererat bite, then he would have received time XP at 2nd level, 1000 fewer time XP, for a total of 3436, which would then have taken him to 3rd level.
He's losing 3436-2999=437 XP, but the chances are he'd not have survived the duergar encounter without the lycanthrope template, so he'd not be around to get any XP (of course, he'd not have been in that mess without it, either).
I suppose the wererat problem, then, has delayed Tank's "real" 3rd level a little (perhaps by one more encounter), but the trade-off is that jaker was able to briefly play a higher level PC than he otherwise would have for a long time. Er, hurray?