OK, so whats the problem, its charging 100 amps which is the maximum,
You have a 1kw load, which is what is causing the 90-100 amp variation
what happens next?, does the voltage ever make it to the Bulk/Absorb transistion ( 57.6 V without a BTS )
It will take about 5-8 hours @ 100 amps to take a battery @ 30% SOC to 80% SOC as an estimate for a 1000ah pack. Batterys are about 80% efficient, so to go from near delpleted to near full charge would take over 12+ hours at 100 amps
I notice the absorb is only 3 hours, that maybe much to short to completely charge the batteries of that size ( aH ), you should check the manufactures suggested charging rates and time.
Please explain in detail what is you issue as I'm not clear at this point beyond having 3 lights instead of 5 shoowing what this issue is.
The lights arer nothing more than a voltage based state of charge ( compenstated when you have a BTS ).
Under load, the lights may indicated a state of charge lower than actual and if you don't have a BTS ( you really need one for your system ) the voltage is effected by battery tempature so that will skew the charge status
Also the Generator must be 240V, I assume it is based on the amps setting and the Volts setting is for each L1/L2 of the AC2 input
Also
http://www.xantrex.com/web/id/1871/docserve.aspx
is the users manual, page 34 ( 2-11 ) & 35 ( 2-12 ) explain how to use the SCP to see the Status of the unit, most helpful for you would be to monitor ( figure 2-6 ) the XW6048 home screen. It showes amps and states to indicated exactly wht the XW is doing