I've also been running into this issue on my Mac (10.9.5). I believe I started seeing this with the 2.4.7 or 2.4.8 release. Unfortunately I don't have the 2.4.7 or 2.4.8 versions around any more but I had an 2.2 release that I tried out. I'll attach two screenshots, one from the 2.2 version and one from when I used 2.4.9 (2.4.10 still shows the same issue).
Is there anything I can help out with to help pinpoint the issue?
Now, after some serious inspection, I think this is related to the R package rmakdown. It causes the same gap whatever way you compile. Please, try to compile just with knit() (knitR package), not with render() (rmarkdown package), and you'll see no gap. Unfortunately, knit() does not handle citations and some other stuffs properly. We are doomed! :-)