if i remember correctly the flashing green means the battery is 80% charged or better. I notice mine sometimes goes straight to flashing green and other times burns red (full charging) for a while. Depends on how I have been riding and how many accessories I have had on.
Check your connections and let it run a while.
You could take the alligator clips and try it on another battery.
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2007 VTX-1300c,, Mustang 75651, HK K2's, Scar, , Progressive Front Springs, All Balls Steering Bearings, Mapam Sissy Bar and Forward Controls Viking Hard Bags with Quick Release Mounts, Reckless Fairing with Kenwood KMR-M315BT Marine Grade Radio with XM..