take a few photos and post them so we can see what this live setup is all about, in terms of physical layout and speaker placement, etc. Perhaps also include a shot of the Main output EQ settings, and comp settings if it is engaged. Is your channel strip Comp/Lim engaged also?
It sounds as though your stage level and the PA are reasonably tuned and appropriate. In this case, if there are no glaring issues with sound quality or feedback emanating from the FOH PA system, if the bass channel EQ looks funny...oh well...just use your ears. It doesn't appear that anything is being harmed or abused, so if that's what sounds good, that's what sounds good.
One of the most difficult instruments to get sounding proper in a PA system is the bass guitar IMHO. It can lack focus and "even-ness" tonally and in level, especially in PA systems where the subs are on the floor and the top end cabinets are flown. (Where are your subs located?). You see, the fundamental notes are living in the subwoofer, but the midrange clarity is living in the top end satellite PA cabinets. I've experienced extreme cases at concerts where you can literally hear the bass notes moving from subs to the flown top end array as the bassist moves from low notes to high notes across the neck. It's almost as though the bass needs it's own set of main speakers, separate from the PA system, in order to accurately reflect the true sound of the bass to the audience via a FOH system.
One of the questions is: do you want the "pump" from the subs, or the "clarity" from the top end cabinets...or both (more complicated)? One solution to this is to have enough power in the mid/hi satellite cabinets to handle the bass at adequate volume down to 80hz, and then leave them out of the subs (crossed over at 80hz), which are then essentially left to focus on the kick drum and possibly floor tom(s). Many bass cabinets will drop off significantly below 80hz (like the vintage SVT 8x10), so it's not as though there is a horrid impact to the bass tone by forsaking the bass's sub frequencies.
OTOH, if you're playing is focused to primarily low note fundamentals, and you don't roam in the mid/high note areas, then perhaps you are better served by subs that are crossed over at 100hz +/-, and keeping the bass focused more in the subs. (110hz is the fundamental tone of an A note, 7th fret on D string or 2nd fret G string.) A lot depends on your sound and the function of the bass in the overall scope of the mix...so...????
