The red flashing light can also mean a bad battery.
I use the small one and never had a problem wit it in 10 years now.
It will also flash when charging some batteries, not sure as why.
Do you plug in the charger then the bike?
I read that can cause it if it is connected to the bike first.
Every time it did it on a battery, the battery was bad. Have you had the battery load tested?
I have had new batteries go out in just a few months.
You said you cranked it and it charged some then you put it on the tender, right? It still flashed the red light.
Did you do a load test? if not I suggest having that done.

 

Hey dobber, i had charged the battery about a week ago...light was green and i rode it monday and forgot to turn off a heated seat. noticed it when i tried to ride to work...no go. hooked it up to the tender and left for work in the truck. was on the tender all day and still steady yellow, indicating still charging. tried to start...not even enough juice to engage the fuel injector pump. jump started it and let it run awhile. hooked the tender back up but still showed steady yellow but the bike started today. rode it about 15-20 miles and the guage on the volt meter runs up to 14-15 and back down to 12 volts when idle. went directly to the battery vs. the pigtail but no difference. I'm beginning to wonder if the tender is bad. I've had it hooked up to my 1600 for a while now and its still steady yellow. battery on the yami was functional and would light the lights.....odd it hasn't gone green yet. will hook up a regular charger tomorrow and see if that makes a difference. Haven't had or done a load test. since i have another battery coming, I might pull it and take it to auto zone and have them run a test on it.