When I got my Stick, I had enough of a budget for it, but no amplification. I thought I could play through my recording software on my computer in my home biz office. I tried it once, and it was cumbersome, too quiet, and lonely (as my office is in the basement of the home).

I have a dear friend who owns a music store, but also has a dog whom I take care of, and he was agreeable to a great barter: boarding his dog over April vacation in exchange for a bass amp. I ended up with an Ibanez SoundWave 80, and it was an ok starter choice, seeing as it has lots of headroom beyond my current practice volume needs, a separate tweeter so its clarity is decent, and a compressor.
Of course, its drawback for a Stick is that it has but one input, so I've been using a Y-adapter to plug my stereo cable into the mono jack.

So far, so good, but I have some volume inconsistencies, even with the amp's compression in use. It's a problem in the melody register. The problem seems to affect strings 1, 2, and 3 more than others, and past the 13th and 14th frets. To be sure that it's not entirely me and my undeveloped technique, I've used consistent fingers and attack levels all around those strings and frets, and the volume problem persists no matter how hard I attack the strings.

I'm starting to wonder if going mono into a bass amp is affecting the volume balance ... or is it simply an issue of my pickup needs to be adjusted? Or once again, is it the fool and not the tool? Thoughts?

I have noticed something similar on my Stick Bass, but opposite to your behaviour... when I setup the Stick in mono (there is a switch) sounds from all 8 strings are equal level, with both sections sounding great. But when I set it up in stereo, (dual input and pre-amp), I need to bump the melody section to match the output level from the bass side...
I have yet to figure out why this is happening, but since I have separate gain knobs, this is not much of a problem...