UPDATE: Tried to see if I could start a new game and just start at ep4, thinking there would be an option to select the major choices (FYI, there isnt).
When I selected the new game slots the previous episodes I had played under the current borked save appeared completed with stats that match my current one.
Tried moving the save into the cloud then selecting the hdd storage. That effectively cleared everything out and allowed me to create a brand new save file.
Deleted that file and moved the backup from the cloud back to the hdd. Save appeared with the same messed up stats, and I was unable to create a fresh new save as the issue I mentioned two paragraphs above persisted.
I'm going to now assume that the save is buggered. I'll complete delete all the save (might as well. They're not the way I had played the game) and start fresh. If, after completing everything through episode 3, the stats continue to not reflect the choices I made, then the issue extends farther than merely a corrupted save.
Just in case, I'm going to cloud backup after each successful confirmation that my choices stuck.
I really hope TellTale acknowledges the issue. It only seems to be a few of us that have the problem (not counting dummies who probably don't realize none of their previous choices carried over) but its a pretty major issue, seeming how the vast majority of gameplay deals with our decisions regarding the story.