Looks like someone else was experiencing the same issue seven years ago 😒 (Re: OSSC cropping part of VGA input?). Sadly they never updated it!

Also found another thread on another forum where this is discussed: https://videogameperfection.com/forums/topic/ … t-9000-cut-off/. Looks like the solution is:

changing H.synclen or H.backporch.

If that does not work with your capture device you can try to set 384p to Passthrough so the capture device receives 640×400 instead of 1280×800.

This will happen frequently on any video card with VGA where it'll be offset to some degree (usually along the X-axis, but also Y-axis) and can generally be adjusted with changing the backporch - that said, I don't bother doing it with an OSSC since 15 profiles is extremely limiting for my collection. OSSC Pro is on my to-do list somewhere.

Another thing is that you won't get any 1024x768 87hz interlaced output via a direct VGA connection to the OSSC - when I've had to deal with ISA cards that won't do non-interlaced 1024x768 I've usually had to do a VGA->Composite->Component->OSSC chain to get some output, though that's far from ideal. 72hz output is generally either squashed in size (most cards) or stretched out vertically by a fair amount (ATi from the top of my head are specific offenders here, but also S3 cards with integrated RAMDACs) along with some fuzziness in image quality - you're better off changing the refresh rate to 60hz to get a significantly more stable image if possible.

Some video cards will have really terrible 640x480 output for anything >=256 colours where colours are very off depending on how much white is on the screen. I haven't noticed any specific trend as to what causes it - I have a GD5420 that exhibits this behaviour, but my GD5402, GD5424 and GD5429 cards are all perfectly fine.

Finally, I have a small number of PCI/AGP cards where the OSSC will sync but will not output anything at 640x480x16 colour mode - I've noticed this with Savage 4 cards specifically, and a couple of others that I don't recall off the top of my head.

It is very possible that the mode you get after leaving Doom isn't the same as the one you had before running it. If you reset the PC, does the crop go away?
If it is indeed a different mode, then you should indeed adjust H. backporch for that mode and store the settings so you don't have to do it again everytime. The thing with PC is that there are numerous display modes, and OSSC might not always give you the best choice for each of them out of the box.. so take the time to adjust the settings each time you get a new bad case, store, then move on. Eventually you'll cover all the cases you typically run across and won't have to worry about them anymore.