Alright, so this issue is really hard to explain.
First, the problem occured with Vegas Pro 15, where I would import clips and it crashed the software, sometimes while importing, sometimes while editing the clip and sometimes while rendering, then I would have to reconvert the entire clip to make it work.
Then I hoped I could fix the issue by buying Vegas Pro 16 and the crashes were no longer there.
Although: When importing these Nvidia Shadowplay clips (60 FPS, Dual Audio Track) the audio would be totally messed up, hard to explain, but all audio was completely out of sync, it did not in any way, shape or form play the correct audio, it was completely jumbled, some segments of audio would play over and over and many more problems.
Then: I fixed that issue by disabling so4compoundplug.dll by renaming it to so4compoundplug.disabled, and then it would be using the plug-in called compoundplug.dll which I also disabled.
And then: it was so close to being fixed, I can see it now uses mcmp4plug2.dll as the "plug-in", that kinda works, but has some issues as well.
There are 3 current issues I'm facing with this, there are certain "spikes" in audio that randomly happen for half a second that I have to find and delete from the audio track. The audio is very often out of sync, sometimes with milliseconds, sometimes with half a second, sometimes the start of the clip is fine, but then during the clip the audio becomes out of sync (THIS IS NOT THE CLIP ITSELF, THERE IS NO ISSUE WHEN PLAYING IT WITH VLC). And the little "preview" or "audio visualizer" is not accurate, when zoomed out, it shows that there is audio when there isn't, when zooming fully in, it is finally accurate.
TL:DR: so4compoundplug and compoundplug are crashing/messing up Shadowplay clips, while mcmp4plug2 is causing delayed audio, small spikes in audio and inaccurate audio visualizer.
EDIT: Alright, so I just found out something. I rendered an entire project (ca. 15 minutes long) where I fixed the delayed audio, but the rendered product comes out with certain parts with delayed audio that was not delayed in Vegas, but the finished product had delayed audio. So I tried, with one of the specific parts that had delayed audio in the finished rendered product, to render it by itself and then it was fine as a 20 second clip. So I guess Vegas just isn't sure where the audio is, both during editing and rendering.