Hi Athlas,
I use Shadowplay for most things, but Bandicam is a solution I am currently looking at for things shadowplay can't do.
I have had a similar problem to CamJgaming myself and figured out that the cause is as you say, the capture software capturing at a specific frame rate but the game playing at a lower, varying frame rate.
The issue I have found is that Premiere cannot accuratly show videos with a variable frame rate. I don't know if other software can, like Vegas or Final cut, as I have not used them. The solution I have found, and it is far from ideal, is to re-complile the video using Handbrake and setting it to compile the video using a constant frame rate. This works, however it does cause some minor stutters in the audio.
Is there another solution that I am not seeing?
Well this issue seems to be a general one, I mean about lost of synchrony. I did open a thread about it and somebody else did it too.
The only thing I can say about it is that I rolled back to a former version to check if it was producing too in all files, and checking different settings.
At the moment I know it happens in any of the codecs I mostly use, H264, Motion MPEG and wrapping them as AVI or MP4.
As more GB of unneeded record are in the video, as more synchrony is lost, and video stops in some scenes.
And about to explain how to do to get a good quality when editing your video I will open a new thread to avoid to mix things in this one.