Sounds like the EP500 is getting full range signal. This could happen for many reasons, but most likely it is because in the 990 you have selected "LFE + Main" to subwoofer or something to that extent. So when the EP500 is on bypass, it has to amplify full range signal, and when its crossover is engaged on the subwoofer, it has to amplify 80Hz and below. The bump in acoustic impact is occuring because of the amp having to amplify full range signal in bypass mode vs. having to amplify signal below 80Hz only when the crossover is engaged on the subwoofer.
The bottom line: Where the crossover is processed should not change the sound of the subwoofer. The two options are,
1) EP500 on bypass, 990 crosses over at 80Hz
2) EP500 crosses over at 80Hz, 990 sends full range signal to subwoofer.
