The 3808 has alot of different settings to eneable and disable the sub so make sure it is enabled in all setup possibilities. 2ch and 5-7 channel etc.

Sean I am not sure what you mean about "Does Audyssey work with analog inputs?" Audyssey doesn't need any inputs to make its tests and the 3808 will apply the Audyssey EQ to all or none as you want.

Jason
M80 v2
VP160 v3
QS8 v2
PB13 Ultra
Denon 3808
Samsung 85" Q70