Firstly want to say thanks to Exeldro for making this plugin. It has been very useful despite it's caveats.
I have found a solution for those who have latency problems between recordings.
Firstly, identify which sources that have the latencies by doing a test recording.
Once you have identified the sources, add a render delay of 60 milliseconds (ms) before the source record filter.
Whilst the sources will still have skipped frames (a little bit of the time being cut off the master-feed), it should now be in sync.
This plugin does cause quite a few crashes, but it happens less when I've added a "-disable-shutdown-check" parameter on my OBS shortcut.
Unfortunately Exeldro has said himself that to rectify these problems he would need to redesign the whole project, which I wouldn't be surprised if he doesn't do it.
So hope this fix is a good one and helps people with their projects!