Unfortunately, my battery bank is pretty shot, so I also start the generator when the battery voltage drops below 44V and then run it until the voltage reaches 59V.
44V! That's far too low for a normal set of batts. My guess is that the batteries are so shot that the SoC calculation in the SI is completely thrown off. For example, the peukert constant would be quite different for new vs. damaged batts, and I think yours are tending towards the latter.
In all, a boost run doesn't happen more than once every day or two because before the SI decides to start the generator based on state-of-charge (SOC) the voltage has usually dropped below 44V. A boost run tends to happen early in the morning before the farm wakes up when the load on the battery bank is low but the SOC has dropped to the point where the SI starts the generator (the SI starts at 45% SOC). I experimented in the past with starting the generator earlier but that then keeps the generator running for such long periods of time that I can't afford the red diesel.
You can control gen runtime through the boost and full time settings. As I mentioned earlier, I'd reduce the boost and full voltages to something like 2.5V and limit boost time to 30 mins - 1 hour and see how it behaves.
If you have a constant 1kW draw and 3kW of PV, then when the batteries are fully charged they're still being hit with a constant 2kW charge- that could easily overcharge them. A 60A charge controller is not that pricey:
http://www.navitron.org.uk/product_detail.php?proID=8&catID=119 compared to the price of a new set of bats.