I've had a similar experience: you booked a 6 night stay but you have only 5 nightly upgrades available; therefore the system will tell you your stay is not "eligible." You're one night over the number you have available.

Depending on how busy the hotel is, they might give you an upgrade anyway simply due to the longer stay, especially if they're not jammed at the time. If they're crazy busy, all bets are off.