Curious question here, but, did you power down the rack before you changed the cards?
The revision level on the output card should have no, none, zero, nada bearing on the situation. There's no configuration to change, no logic, for all intents and purposes they might has well not even marked the revision change on the piece, for your purposes they are identical, NOTHING AT ALL TO DO EXCEPT CHANGE IT OUT!
Reason I ask is that if you did indeed power down the rack, then nothing that you've listed here should be happening at all. NOW, that being said, if you did NOT power down the rack, then there's no telling what will happen, or what you may destroy.
Case in point, recently one of my I&E techs discovered a faulty thermocouple card in a data acquisition system. It was running on an SLC 5/03. He quite literally forgot that the SLC family is not hot swappable, and simply pulled the card out replacing it with a new one.
About an hour later, when he cam and found me, we determined that not only had he ruined the new thermocouple card, but also the rack and the processor. Now, this was a little odd because usually it doesn't get the processor. But, toasting the new card and the rack is quite the norm.