I'll start out with saying knock on wood as I'm not sure yet, but the save issues seem to be fixed. So far both saving and loading saves have been stable again. Not sure what caused/fixed it, but my current hypothesis is that it was dirty edits causing it so fixed by cleaning esp's. If so, the lesson learned is to always check/clean added mods with TES4Edit, which of course is nothing new but I have been rather sloppy with it, thinking that it probably won't cause any severe issues if a couple of esp's have some dirty edits.
Also, I doubt it was connected to streamsaves specifically but rather made saving a bit unstable in general, which also affected streamsaving.