Is this normal? My cat with fleas and flea allergy dermatitis won't use the litterbox

One of my cats (3 year old, neutered male) has a history of stress and anxiety behavior related issues. We haven't had any problems in a long time though, until he recently came home from the vet with fleas. He's been lethargic and uses the bathroom all over the house (he hasn't used the litterbox since coming home). He's being treated for flea allergy dermatitis and an ear infection - we went back to the vet on Saturday and he came home Monday. Still lethargic, still not using the litterbox. The lethargy is completely out of character, as he's normally into everything and follows me around, and loves being on the screened in patio outside. He's keeping his distance too, which also isn't normal for him - he normally sleeps in the bed with me and cuddles on the couch and is also super playful.

Could him being sick and having the allergies that he does to fleas be causing him to not use the litterbox? I know he's miserable, and he's been treated with Capstar, Advantage II, and his regular fluoxetine. Since the ear infection, the vet gave him ear drops and two injections - one for itchiness and discomfort and one for pain. I'm really worried and am waiting to hear back from the vet on if there's anything else that can be done other than just waiting it out and cleaning up after him. I'm assuming that once he starts feeling better that he'll return to the box?

Has anyone had a similar experience or heard of anything like it before? Since I'm relatively new to cats and this is my first time dealing with fleas, I just want to make sure I'm doing everything I can or to see if the bathroom issue could be tied to him not feeling well? How long does it normally take for them to get over something like this?

What did you hear back from the Vet?  This is NOT normal for him not to use the box because of flea allergies.  Sounds like something else is going on.

They ran all the tests and besides the miliary dermatitis and the ear infection, he was given a clean bill of health. They believe it's tied to his stress and anxiety behavioral problems.

Seeking their professional opinion now on how to move forward, because we've tried a lot to manage and deal with this issue for over a year now. 

Lethargy is NOT normal, and I've never heard of that particular thing being caused by stress .  Peeing outside the box, yes.  But not lethargy.  And you've never witnessed that from him before either, right?   You did tell them he was lethargic, correct?  That's my main concern right now...perhaps he's having a reaction to the flea meds.

As to the litter box avvoidance, since this is not new, I guess you know the ropes?  Here's a good article in case you haven't seen it:  http://www.thecatsite.com/a/how-to-solve-litterbox-problems-in-cats-the-ultimate-guide