On these things, just like on most modern computer controlled engines & vehicles, 12 volts in a battery for all intents and purposes means that battery is
FLAT, while anything over 12.8v showing on a rested battery is considered 'Fully Charged', altho if it's
just been taken off the charger in the last 10-20 mins or sso, it should show something closer to 13.8v to be considered fully charged!! :lecturef_smilie: So your digital gauge/meter/whatever showing 12.3 volts as being just 50% State of Charge is pretty close to right.
That initial '100% charge' before your ryde probably wasn't much more than a 'Surface Charge', resulting in the Check Transmission warning you got not too much later, but the longer run after that should've been spot on for giving your battery a 'proper' deep & closer to truly 'full charge'....

hyea:
So with any luck, that will be the solution for now - but you need to consider what caused the initial poor state of charge that kicked all this off in the first place! If your battery is the original from 2012, then it's well past time to replace it - now that you've had one 'flat battery incident, you'll probably have more on an increasingly frequent basis until you do!

However, if your battery is relatively new, you might want to get your battery tender/maintainer checked & replaced if necessary; put your battery on a good quality 'smart charger' for about 24 hours or so every couple of weeks; &/or ryde it for 30-60 plus minutes at Hwy speeds once every week or two - keeping a battery on a tender whenever it's not in use can easily hide a failing battery such that it'll start fine when you leave home, but unless you give it that 30 plus minutes of solid ryding before stopping it again, you'll be risking the battery depleted by that first start not being charged up enough to kick it over again, leaveing you stranded maybe 30 mins away from home! :shocked:
Proper 'Smart Chargers' with both Maintain & Condition cycles in their charging program are better than the old style 'trickle chargers' and many newer 'non-smart' battery chargers &/or tenders too; but none of those should really be left connected to your battery
ALL the time, altho doing that might keep the battery charged & useful for a while, especially during a short winter lay-over. The best thing you can do for the longest life of your battery is give it a good ryde of 30-60 mins or so at open road/Hwy speeds once every week or two... hard if you live in snow country I know, but if you can't do that, then you should probably start thinking of replacing your battery every third or fourth year unless you like contending with battery failures that can 'apparently' happen out of the blue, even if your Spyder started fine & was running OK right up until it just didn't any more! Even just turning a corner might cause the DPS to suck enough juice to cause the computers to shut down - and once that happens, good luck trying to start it again without a jump box or help!