There's a few other interpretations available as well. The statement "there aren't too many geeks either" following your conversation about the quality of engineers might be to register surprise at that (perceived?) fact. Usually when I think of a highly competent programmer the mental image is of someone a bit geeky. If your company has a bunch of competent engineers that aren't geeks then it is an outlier.

It also could be viewed as an expression of regret. Maybe your co-worker is a closet geek himself and is upset that there aren't many to be found in the office. He might have been trying to commiserate on that situation. He might not even have identified you as a geek and could have meant the comment purely to express his feelings of loneliness.

I know the programming maxim is "be liberal in what you accept, and conservative in what you send", but even that principle fails when a course of action is undecidable from the inputs. File this away for a while and see if any clarification happens, if not forget about it. Or don't, but that's my advice.

Anyways, back to my spring break Firefly and programming marathon. Good luck with your refactoring. (By the way, any details available there?)