I don't know anything about your processor. However, the processors I work with intentionally do NOT run their non-sync audio through subwoofers. Also, you might miss out on the heavy thuds & bone-jarring vibrations, but the subwoofers I've been around wouldn't normally leave a room that noticeably flat.
Whether there's actually something wrong with the sub or not, I'd bet something else is going on with your system.
(edit) A properly installed reader rarely needs to be touched (other than routine cleaning) If the LED and the pickup were properly locked down, what's to change about the alignment? Not much... and if it were, you'd lose your highs first... not your sub-lows.
The lateral guide could go out of alignment, but that would show up as buzz of one sort or another... not a lack of low frequencies.
[This message has been edited by rodeojack (edited June 01, 2005).]