Just to clarify, Audyssey doesn't "set" the speakers to "Large" or "Small". It measures the -3 dB point of the speakers in the room and reports it to the receiver. The receiver *manufacturer* decides what constitutes a "Large" or "Small" speaker. Onkyo uses 80 Hz. IOW, any speaker that has *any* response below 80 Hz is set to "Full Range", (AKA "Large").
Audyssey actually recommends that they be reset to have a crossover engaged, which is Onkyo's terminology for "Small". When they are first reset off "Full Range", the suggested crossover should come up. You should not reset the crossover below this setting as Audyssey will not correct below the -3 dB point of the speakers. This would involve boosting the levels below the -3 dB point, which could be dangerous to amps and speakers. The crossover can be *raised* and Audyssey will still EQ the entire system. However, it should not be *lowered*.
Audyssey is working with the numbskull's at the manufacturers to get them to change how they determine whether a crossover will be engaged or not. So far, they've convinced Denon to use 40 Hz. Onkyo is a little behind on this one, as are some of the other manufacturers.
To the OP: Until you get the new sub, I would follow Russdawg's advice and run without a sub. Once you get the new sub, re-run Audyssey and, if it set your speakers to Full Range", reset them to the appropriate crossover.
For more information on Audyssey, please see the "Official" Audyssey thread:http://www.avsforum.com/avs-vb/showthread.php?t=795421
Chris Kyriakakis, the Founder and Chief Technical Officer of Audyssey posts there all the time and is *very* helpful. Also, there is a document being constantly updated showing all the little tricks and details to properly set up and use Audyssey.
Russdawg, your inconsistent results with Audyssey can probably be made more consistent by following the setup procedure documented in the Audyssey thread. Good luck.