I'm a recording a BBC radio 5 live stream. I've tried both
Jaksta and
WM Recorder two times.
It's interesting you say that they should both record in VFR if the source is VFR. When I mux the video stream from the flv file and open it in VirtualDub (I have to because the flv container makes Vdub crash) I must set both WMR recordings to exactly 25fps to make the audio sync and the Jaksta recordings to 25.00x. (Indicating that the WMR records in CFR.)
I've uploaded the timecode files, extracted by FLVExtract from the original recordings. Maybe you can interpret the data in some way.
http://www.4shared.com/file/ApmVQR7T/timecodes.html