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Update, I’ve resolved most of the issues today. tl;dr user error 🙂

– Issues on AV1
I was not aware that scart has input and output on some lines (Or, I was but it didn’t register that this could lead to them being wired backwards), and my cable was wired for “SCART>BNC” Rather than “BNC>SCART”. This resolved the issues using RBGS as well as the lack of audio. I should have caught this while pin testing the cable. The seller did mention this in their listing, and offered to fix it for the cost of shipping, but I’m impatient so I had my much more soldering competent roomate switch them around real quick.

– Jailbars
So far not present with AV1 with my limited testing, so I’m now fairly confident that it’s an issue specific to the VGA>BNC cable I was using. I had also found some interference that manifested in moving horizontal lines on the screen, also gone now that I’m using the higher quality SCART cable. I want to mess around with the LPF just to make sure but I’m 99% sure this was entirely a cable issue.

– Aspect ratios
Still need to investigate this, but I’ve gotten my capture card to accept the correct aspect ratio so that’s not a huge deal. Very likely this is a setting I haven’t messed with yet.

– Interlacing/deinterlacing
The behavior I was seeing is isolated to the capture card not being able to process the interlaced signal particularly well. Using an HDMI splitter I see the same signal on my monitor with a steady flicker as expected, whereas the capture card creates a kinda inconsistent wiggle. I’m using a bargin basement capture card so this isn’t a surprise, just wanted to confirm what was going on.

– Picture dropping on input signal change/signal not being sent on startup
I need to test this more but I managed to get the capture card to drop picture once or twice today while the monitor was still showing output. Both devices hooked up to the OSSC via HDMI splitter. So this seems to be some issue related to the capture card specifically.

– Sync dropping on OSSC on input signal change
This hasn’t been well tested yet but I’m fairly confident that it’s an issue cased by interference on the VGA>BNC adapter. It happened on a somewhat regular basis with that cable, albeit inconsistently, so an evening of PS1 games should determine if that’s still happening or not.

Needed to hit up support to realize I had the wrong scart cable, so I can’t take credit for figuring that one out. But now everything is working more or less as expected. I’ll post another update once I’ve figured out the rest of the problems. Never know when your forum posts will turn up in a search result 7 years later.