I hope I don't sound too rash in saying this...
So I think it's really good practice to learn how to accept compliments graciously, especially when you know that the intent behind the compliment is good. I can understand struggling to receive them as truth, and while they may not necessarily be 100% true for you for specific reasons, the point wasn't to make a completely truthful statement about you that was meant to be scrutinized, it was simply an attempt to encourage and build you up. (And let's be honest, we can all use a little extra encouragement during the day.) So for me, I've been attempting to lose weight for the past 4ish months, and I've been successful so far. When someone compliments me on that, my first reaction is to think that I appreciate it, but still have a long way to go. When I react that way, though, I'm focusing on myself that much more instead of turning my attention back to the other person in appreciation of their kindness. That's why I just try to meet those compliments with a warm "Thank you, I really appreciate that." So the part that I hope doesn't come across as rash is that I think an inability to receive compliments well can actually be a form a pride in that you are only focusing on yourself more in rejecting those compliments than if you simply acknowledge the kindness and receive it for what it is (given that the intent behind the compliment was good).
I think I see it this way also because I enjoy complimenting other people and I'm always a little bummed when I feel as though they weren't able to receive it. I'm never out just to flatter, but I like to encourage, and if my encouragement doesn't work then it bums me out!
Edit: One more thing I might add. An alternative to not receiving a compliment could be also to get in the habit of receiving it and giving the credit to God. If you can sincerely respond in that way, that's always a great thing to do as well.