It could have been highly complimentary. But it could also have meant “I just don’t believe that you are as wonderful and virtuous as you appear. You must be a phony.”
If it were said in a romantic context, I would definitely look for the double or hidden meaning. I would expect the speaker to have in mind the thought we’ve probably all been taught: “If something seems too good to be true, it is.”
The suspicion might reflect on you, but more likely it reflects on the speaker.
On the other hand, they might just have been mouthing a cliché without expecting you to seek a deeper meaning in it than “That was great, thanks.”