Hmm. A dual-x-screen created via those scripts should work equally well as a pure single display / single x-screen setup. Unless the problem is on the side of the monitor, which looked very likely from your description - but then the problem should not go away just by using a single-display setup.
After using XOrgConfSelector again + logout/login to switch to the dual-x-screen configuration, can you provide the info i requested in this post and following ones:
https://psychtoolbox.discourse.group/t/vbl-vertical-retrace-syncing-problem/3589/13?u=mariokleiner
Iow. the generated config file, the log output etc. Also the output of PTB in Matlab, e.g., for PerceptualVBLSyncTest. You are using the standard Ubuntu desktop GUI of Ubuntu 20.04.1-LTS, right? And no error or warning messages from PTB?
-mario