I just figured out the problem....something i didn't know would be an issue.
At the top level, i'm switching between different pieces as I said before. 2 pieces of pipe, 1 piece of pipe, 1 pipe 1 plate, 2 pieces of plate, etc. In all i've got 7 different pieces i'm switching between with ComponentReplace. That part never had any issues until today.
I had just started to add those 4 pieces that were all showing up in the first of the sub-assemblies i was switching between. And that's where the problem began.
As it turns out, of my 7 choices, all are assemblies - but one. When I set it to a single piece of pipe, i just used the ipt file because it seemed kind of pointless to make an assembly for a single part. Turns out, though, that i could swap between the assemblies and the tip pieces that were supposed to be off stayed off and the one that was on stayed on. When i swapped to to the part file, it apparently would break the connection between the assembly file and the top level forcing all pieces to be on and visible. With the connection broken, nothing could restore it other than deleting the assembly from the top level and reinserting it. Didn't make sense that that could be the reason, but when i replaced it with an assembly it was fine. I've switched between all the options now and haven't had it be incorrect yet.
More ironically,the one part file was the piece i had planned on adding the different tips to next. Had I started there instead there'd have been no problem
Now, just 'knock on wood' that it's the actual permanent solution