If your subwwofer is connected to the receiver's subwoofer output, it will only receive sound in the 0.1 (LFE) channel plus any redirected bass from the other speakers. The receiver's crossover will eliminate, effectively, the higher frequency sounds from what gets sent to the sub. That's pretty much the point of a crossover . . .
Sounds like a HTIB sub, though. If so, the sub itself may have an unbypassable crossover, and stacking it with the receiver's crossover may result in a frequency range that is too low in sound pressure level.