I have some albums that are all FLAC except for some iTunes exclusive bonus tracks that are m4a AAC. These albums play with sweet fades instead of traditional gapless.
My ALAC albums with AAC bonus tracks don’t have this issue, which is why I think it’s an issue when albums have tracks with different containers.
Edit: This also happens with Compilation albums, even when all tracks are FLAC.
Codec doesn’t matter at all. What matters is consecutive tracks. If you’re missing any, it’ll assume you’re not playing an album in order and apply Sweet Fade.
Plexamp logs would tell exactly what it’s finding out of place, if you upload them right after it happens.