Zerk isn't being cleared on level transition. EDIT: The same situation happened again and this time zerk did get cleared. I don't know why it didn't happen the first time, but the second time I had a different issue of having extremely low strength at the start of the next level.
I'd also like to file a formal complaint about the current spiritual armor mechanics.

Any time it saves your life, the excess damage gets converted to treated wounds. Reasonable enough when it's rifles and shotguns. Explosives do this and leave you stuck in permanent incap. Zerk is the only way out, and that only buys you the time you have to get to the exit so that level transition can clamp your wounding and fix all but the last 90% of that. I'd still be able to recover from that if not for the aforementioned zerk issue. I now find myself spawning into the next level, still zerked, with only about a minute to clear out the hot start, chug my entire potion, and then die a slow death from comedown anyway. If I didn't have the autosave for the previous level, the entire campaign would be down the drain.
Honestly, I'd rather just have the shield cores in id and never have to deal with this again.