Being a transsexual, the very existence of this trope not so much bugs me as annoys the heck out of me, to the point that works which (realistically) portray the negative consequences of involuntary sex-switch feel like a breath of fresh air.
I agree. In a lot of gender-bending, or body-switching, situtions the character seem very comfortable. No dsyphoria, no nothing.. No one even thinks to just transition back into their gender the way a Transsexual does.
since this trope is most frequently invoked in the conclusion (where narrative causality is no longer relevent) I think it more likely stems from widespread endorsement of The Mind is a plaything of the body, particularly in cases where the transformation is total rather than cosmetic.
There is also the possibility that the Gender Bender candidate was a transsexual in denial and that he got a free AND flawless sexual reassignment surgery, and just needs time to adjust to his new body (brutal change could need some time to get used to, even if it was what he/she wanted). I don't know in how many Gender Bender stories this explanation could fit (maybe not that much), but there gotta be some leaving it as a possibility.
Maybe the idea of transitioning back doesn't seem worth it. They would rather remain in the new body than pay $1000s of dollars to get something resembling (but not quite equal to) their old form. A lot of prospective transgenders don't transition (or don't transition completely) because they want a flawless cisgender body, an unwilling gender bent person may be the same.