I had a love/hate relationship with compressors for a long time... as in, I loved to hate them. Once I got the Symmetry, I was able to FINALLY wrap my head around how to best use a compressor. Might be worth some further exploration, as compressors can help with a wide variety of things.
Aside from getting your bass to a PC and seeing the visual representation of the waveform when you record, I can't think of any other ways to measure individual string output. Even then, it's a ballpark solution at best to the best of my knowledge, because that beefy low E is going to have more mass and frequency output than a G string. But, it might be helpful to further understand your bass. I did that when I replaced the pickups in my Jazz V, and found that there was a much thicker low end.
(see illustrations below). Those pickups in your G&L may just have more low end than you actually realize, or that you can necessarily hear. I know the Quarter Pounders did. If you're hitting the Effects that hard, it may account for the problem you're having. Do you have another bass you can try?
Possible solutions for people having the same problem as Dade:
1) You could add a compression block before the filter, set it with higher compression settings than you normally use to squish your sound more than you normally would, and program it to the same footswitch as the Auto Filter. That way you can have your normal tone when the Auto Filter/Compressor combo is off, and the extra compression when the AF is on.
2) You could also try adding a 10-band EQ block before the Auto Filter. Then try dialing down one frequency point at a time to see where the trouble spot(s) are. Could be that your upper mids just need a little help, or could be that there's some serious low end in there that you don't know about from those pickups. You could also use the EQ block in combo with the Auto Filter as well... Program the EQ to only be on when the filter is, and goose the frequencies that need help.
Not sure about the +6dB boost, but if it works, that's what the setting is in there for. I just suspect there's something going on with how hot your signal is. Do you have trouble with signal based effects, like dirt?
5sg.
Stock Fender MIA pickups:
View attachment 3182223
Seymour Duncan Quarter Pounders:
(Note the much increased low end frequencies)
View attachment 3182225