Voukoder R2 produces x264 video with Incorrect timebase. I encoded 10 seconds 59.94 fps video using Voukoder 2.0.8 and 1.2.1 in PrPro CS6, Some video hostings consider those videos VFR. I have very limited knowledge in this area and am not sure if I understand this problem correctly. But i think it appeared in 2.0.0-beta1 release and could be related to this issue.
Here are ffprobe output:
codec_time_base=1001/120000 (in my understanding this is correct)
codec_time_base=599599/72000000 (In some other tests I saw different weird numbers)