Biometrics has good advice on the low voltage fault, it is possible for a new battery to be a bad one. Are you sure it's a low voltage fault? That one should not require a reset - it clears itself.
Check the codes. Before you do a reset.
The low voltage fault can happen with a low battery & can be confirmed from the saddle if you do the rolling restart - see Anton's site
and click on the ABS Faults article under brakes (you have an 1100RT, so you have the early ABS2 with the three pin diagnostic connector). The rolling restart is described under fault 5 - low voltage. That may not be the fault you have, so replacing the battery won't necessarily help. If it is actually just the low voltage fault then you need to problem solve your battery, possible current drains as Biometrics mentioned, charging system and the connections between them all and the ABS/Motronic unit. Since your bike sat a bit, cleaning these up could help - look for corrosion at the starter solenoid too - if there's resistance at that connection, there will be more voltage drop as the starter spins and thus more chance of the error.
This is all assuming that you've a low voltage error. Does it blink appropriately when you turn the ignition on (both flash together) and then switch to alternating after you start the bike? If no, then you have another problem and not the just the low voltage problem.
Again, check the codes:
Read Anton's pages and go to the IBMWR Oilheads tech articles
, and download the R11xx maintenance manual. Worth having, regardless! Detail on the ABS is found around p 71. & this is the source material for much of Anton's. Only part that's any challenge is the test equipment - you can make your own with a 12V led or a 5v LED and a resistor, OR use an old analog voltmeter if you or someone you know has one (really, really easy and way cheaper than the GS-911 you'd need for a 2005+ bike). Follow the procedures and read the codes. Then get back to us when you have more information. You can use your new (or existing) test equipment to also check the codes for the Motronic unit.
I sure wouldn't give up on the bike without first reading the codes and then making efforts to repair whatever the trouble is. If it's a persistant low voltage fault in spite of a good battery and charging system, I'd start on a search and destroy mission for corrosion, loose contacts and loose and or corroded grounds. Other codes may point you in other directions.
I have an old analog voltmeter if you and the bike are in the Ellicott City area, but a trip to Radio Shack might be more convenient to you! Good luck.