Yes, certainly it means he's not enjoying it, he's having a bad time, but the specific sense of "come back to bite (him)" is that he realises that all these negative things are the result of the deciding to take the job: it is his idea of getting the job that has come back to bite him. So the emphasis is on the idea that this decision has has unpleasant consequences. All the bad stuff he's living through now is the result of that decision. So the emphasis is on the fact that it was a bad move to take the job in the first place; he has unwittingly caused himself all this trouble which makes it all the worse.

"Come back to bite" is an expression that conveys above all unforeseen negative consequences of decisions people make, specifically unforeseen costs to themselves.

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Note added at 1 hr (2014-06-28 11:29:51 GMT)
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"Come back to bite" very often has the sense of paying the price for our mistakes, sometimes with the idea that we did something wrong to gain some advantage and it's turned out to our disadvantage. You can say that someone's lies have come back to bite them, meaning that those lies are now causing them problems. Metaphorically it's the idea of using an animal to bite someone or something and then having that animal turn on you and bite you. "The biter bit".