There are a LOT people on this forum who successfully sync Clocked to external gear and have been doing so for literally years. Believe me your experience is an unusual one that I would like to understand.
Please post a video like the one you have with Marbles above but show the clock coming out of Marbles (which works with Clocked) and the clock coming out of the audio module which goes into marbles (which you say doesn’t work with Clocked) on the Scope so we can see if there are any obvious differences.
Please also show what happens when you try and send the clock from the audio module directly into Clocked.
One other thing to try - take the clock from the audio module and send it through a utility like MIX from VCV (instead of Marbles) before going into Clocked and see if that works. That would result in the same clock being passed through but just 1 sample later. If that works fine when connecting to Clocked directly doesn’t, then that might give us some clues as to what is happening.