You may not be able to check in online if:
- Your reservation has changed (flight cancelled)
- The computer isn't able to bring it up (too many segments, other error)
- Other reasons ?? (the above two have happened to me personally)
You are NOT on the upgrade list until you check in. But the upgrade list is just that (a list) until the battlefield upgrades process, which will happen just before and during boarding at the gate.
Don't confuse the upgrade list with EUA upgrades, which are separate - when the EUA agent runs (5, 3, 1 day out, plus possibly when R seats free up) it looks at everyone on the flight by elite status, regardless of check-in status.
I actually had the same errors this weekend, but between when I first tried to check in and when I actually checked in at the airport, did get upgraded anyway despite the error messages.