Psychological Reaction to Meds?

Rambi has a 'cold'. The vet gave us Baytril twice a day for three weeks, plus Metacam and Cisaral for as long as necessary. We are now two weeks in. I stopped with Cisaral after a day, because Rambi was eating and toileting fine. After a week I stopped with Metacam because he seemed happy and pain-free. I am still using Baytril.

The problem is Rambi HATES being picked up. It is easy enough but he is now scared of me and my husband. When we have him he is fine, just sits and munches on whatever we give him as a treat, but he runs away from us now. I am hopeful that this will reverse after the meds have stopped, but I am worried that he is behaving differently. He is sitting in one of his hidey-holes more than usual and isn't eating as much hay (although he is eating and toileting, just not playing with his food as much as usual). I fear this is because he thinks he is at permanent risk of being picked up.

I am at a loss what to do. Anybody else experienced this before? I am taking him back to the vet (the proper bunny-savvy vet - he was on hols when Rambi got sick) for a check-up next week, but thought i'd ask here for some health-related behavioural advice.

Thanks

Emma