I have my guitar on the lead channel and:

I am in D and when I switch from a power chord from the D to A the A one sounds flimsy, like really weak. When I play around with the settings they both sound very bassy. What do I do?
personally turn down the treble and turn up the mid a tad and that might help but also check ur in tune perfectly and if that doesnt work it could have something to do with your intonation
Let us know if that works - I would say raise the mid.
It might but be a tricky fret - does it sound that way when you play powerchords in E on that guitar?