I don't know if there's a way to solve this technically, maybe something to do with resolution settings and your monitor.
As for aiming advice, here's a few handy tips.
I'm going to assume your long tom stays in passive so as to avoid counter-battery fire from other long toms.
When you flick your radar over to active, it shows on the radar the 1250m range of your BAP, as well as any enemies within/close to that range.
There's two things you need to do quickly:
1) Determine which target you want to fire on (heavies, tanks, assaults, other long toms). This means you need to cycle very quickly through available targets while noting their movement on the radar.
2) Determine the range of your target. This is done mostly by estimation to limit your vulnerability when in active radar. Now, in order to estimate range, keep in mind that the passive radar circle is a 300m radius and the active (for long toms) is 1250m. Using this, as well as the radar grids, you can roughly guess range; you'll get more accurate the more you practice.
Once you have these two pieces of info, line up the blue line on the radar (the direction the artillery is facing) with the location or estimated location of your target, then flick back to passive. Raise or lower the barrel to get the range close to your estimated range and fire. You can flick on and off active radar a few more times before you fire to get a more accurate shot. Once you fire a few shots or destroy your target, MOVE. Do not stay in the same place.
Once you get good at this method, you can snap disturbingly accurate shots off from seemingly nowhere, all while limiting your vulnerability and staying mobile.
EDIT: If your target is a suspected poptarter that is stationary but effectively using cover to block long tom shots, try lifting the artillery barrel up past the 45 degree mark. You'll notice the range will increase to 1500m, then start dropping again. What this does is give your shot a lot of hang time, but makes it come in at a much sharper angle, effectively negating any cover.