So when running on the newer versions of sar (1.12.4-5) I have issues with portals linking between timelines, I have no issues with this on the older versions of sar (1.12.3) though.

You should try newest SAR version and see if it fixes your problems. https://github.com/p2sr/SourceAutoRecord/releases/tag/1.12.6-pre13

Also make sure you're on the "release" beta branch of the game on Steam. (right click -> Properties -> Betas -> select "release")
SAR targets this version of the game, since that's the version we use for runs.

Thanks for the help! Everything seems to be working fine now.

So uhh, after playing around for a bit the issue still seems to be here, is there anything else that could be causing this issue?

You should join the discord and ask in the help channels.

Will do! Just one question though. Would I ask in gameplay help or technical help?

technical help