First, I did do them one at a time - in fact, at the first install, I only got a single SCard.
Successful install here the second time around.
The original card would work in slot2, but not slot1.
I removed all cards.
The installer plugged the new card in. It was instantly different - instead of "Card not operating normally", we saw the CableCard Menu. After a few min, the ID screen came up, and activation went without a hitch.
Plugged the already working card back into slot2, both are working.
I guess I have to blame the card. I still think that if I swapped the cards (with my service it seems they don't care about hostid - it's already running in a different tivo from the one it was activated in) -- I'd bet that the "bad" card (currently slot2) still wouldn't work in slot1, but the new/good card (currently slot1) would work in slot2. Seems to be a specific combination of card and port.
In retrospect, I wish the TSR hadn't been so quick to replace the first unit - there was nothing wrong with it. They hardly asked me any questions or made any attempts to troubleshoot, but then again, I only had a single card at the time, so there's not much I could have done.
I'll certainly keep a wary eye on it if I encounter any other problems, in which case I'll try the deactivate / reactivate approach.
All's well that ends well, I guess. I hope the OP has resolved their issue...
PS - To respond to other comments, guided setup was run between cards - but only because they happened on separate dates. I doubt I would have been patient enough to go through Guided Setup between two cards installed and activated one right after the other (It takes 20+ min to complete!). That's useful advice.
For the rest, I'll explain the "Card not in normal operation" error.
TiVo says "Scard inserted", but I immediately got 161-4 errors (which I tried to ignore) about every 3 seconds. "CableCard Menu" simply says "Card not in normal operation", and no other menus are there (Pairing, Conditional Access, Status, etc.) NO card, host, data ID screen EVER appeared (so how could the tech do anything related to pair / auth?)
After letting the card "cook / soak" for 24 hours at the advice of a TSR, the 161-4 errors no longer came up, but the menus never appeared.
The same card came right up in slot 2.
Lastly - technically, the "problem" persists - that card doesn't work in slot 1. But since it's fine in slot 2, and I got another card for slot 1, it doesn't much matter anymore. Still, I hope this info might help someone else.