I'm sure this coworker is annoying, but I agree with the PPs that this doesn't seem like such a terrible question. If I were in that position, I would just say, "No they're from my sister. Isn't that sweet of her??" It would really not occur to me that the implication was that my SO didn't love me or my relationship was lacking in some way.
I have noticed in myself that when innocuous-seeming question start to really bother me, it's because I am feeling insecure in that particular area. However, since I am married (and have been for almost 7 years), a question about whether my husband or someone else sent me flowers would not bother me in the least. I also personally don't care when people ask about my husband's and my reproductive plan. I'm not bothered by the fact that we don't have children yet, so I'll just answer people without being bothered/annoyed by their questioning. But the minute someone brings up exercise, diets, if they complain about their own weight, etc - I immediately start to tense up, even if it's not directed at me. Because that's what I'm slightly hung up about.
OP, is this something you relate to, or does your annoyance have mostly to do with the source?