I need advise, please...

Been having a weird intermittent starting problem on 2007 Sportster XL1200L that is getting worse. After sitting for a day or more, try to start it and it cranks over fast, but won't fire, can crank until the battery is dead. Put it on a 4amp charger for about an hour and it will fire right up.

Replaced battery with brand new one last week. Although, Harley tested the old one on their new fancy battery tester, and the report said it was still good at 203 CCA's - still I replaced it because it died after about 30-40 seconds of cranking.

Did some troubleshooting today when it would not fire and found I had no spark at the plug; pulled the plugs and while connected to plug wire and grounded to the cylinder during cranking and NO spark, weird! Brand new plugs, BTW, just thought it was inexpensive thing to try.

Checked the DTC codes and found nonE accross the board, weird!

Checked for voltage coming out of the coil while cranking, and no voltage, which indicates coil is good.

Got frustrated and put it all back together and the battery back on 4amp charger and went to a movie with my son (GI Joe 2, meh it's ok).

Got home, took it off the charger, and it fired right up, WTF?

What the heck could be wrong, no DTC codes, but could it be a weird intermittent coil issue, ECM, CPS, what could it be? Thoughts?

Any advice welcome, and thanks for the time.

 

Found the root cause was my Power Commander III. When I had no spark, I removed the PC from inline, and reconnected to the stock ECM and it fired right up. Bummer, now what, another $400 PC, or $200 & just go back to HD to download standard Stage 1 map to ECM.

UPDATE:
Took PCIII off bike, imported existing map and saved file, downloaded new firmware version. Flashed the new firmware, and redownloaded original map (which was dyno tuned), and reinstalled. Still had intermittent problems starting.

Found this on PC's FAQ section:
I am having trouble starting the engine when the Power Commander is installed.
Most Power Commanders are powered by the injectors on the bike. When you turn the key on, the fuel pump gets power and primes the fuel circuit. When this happens, the injectors get power, and the Power Commander also gets power and lights up. After a few moments, the fuel pump has pressurized the system, and usually shuts off. If the fuel pump shuts off, the injectors’ loose power, and the Power Commander shuts off. If you attempt to start the bike when the Power Commander is off, the bike may take longer to start than normal, until the fuel pump comes back on. The fuel pump may come on instantly, after a few engine revolutions, or on some bikes seemingly not at all. If the fuel pump does not come on, the bike will not start. We recommend starting the bike once you turn the key on. Do not wait for the fuel pump to shut off, or a check engine light to go out.