I haven't read through all the replies yet and I don't know if you've gone back and tried to talk to her yet but here's my advice:
Send her an email or go round to her desk and say "hey got a min for a tea or coffee? I wanna talk to you about something".
In my office, there's a tea/coffee cantine so it's usually a good few minutes walk to it which is an ample opportunity to be nice and be yourself, the person she knows, and talk normally.
When you have your tea/coffee sit her down and just say it straight up like it is...
I think we get on very well and we have a genuine friendship which is rare and I hope that you feel you can be as completely honest with me as I feel I can be with you so that's why I wanted to say that I get the feeling something's changed. You seem to be a little distanced around me now and I'm just wondering if it had something to do with the compliment I paid you the other night when we were having drinks?
This will show her that A) you're not a baboon or a brute B) you're aware of yourself, what you say, and the effect it has on others C) you're mature enough to deal with what you perceive to be an issue head-on.
Re-assure her that her answer won't affect you either way, that you just wanted to make it clear that you were paying her a compliment because you meant it. It doesn't mean you want to date her or become 'more than friends'. Just be clear in that her company makes you feel comfortable and you only pay compliments to those you're comfortable with because otherwise someone not as close to you might misread it.
See what she says and respond accordingly.
In my experience of interacting with odd girls, and believe me I seem to attract all the nutjobs in the world cause every single one of them has had social and communication issues, I find the best policy is honesty. Just put it out there because she's one of two people. Either she'll be put to ease with knowing exactly where she stands or she'll revert even more and react negatively. If she does the latter, in my opinion you're doing yourself a favour cause it would've happened sooner or later.
hope it helps