Hello there. I have bongo 5 HS . Have the same problem. I use Ampeg svt3 pro. But I have reduced the problem with this idea.
I figured it out that EBMM Bongo EQ settings are so madly powerful and especially the bass-boost pot. So, I use maximum let's say, not more than 75% of bass pot on my guitar. ( my settings on amp are flat - except middle pot which is reduced at 30% ) . And I was experimenting with everything and I think that only that pot is little problematic. So , do not turn it all the way down, but only at half - and maybe more 20% from half ( flat ) ...
Also, lower the magnets, at for example 5-6 mm from bass string ( treble string 1 or 2 mm higher ) - that's for HUMBUCKER. Single coil they reccomend little lower, but I prefer same -or even higher - maybe 1 mm higher
That's how I THINK, I solved my problem
