912iS Battery not charging but engine stops when load applied

Did you still have your start power switch on at the time, or was it already turned off?

Is this a new unflown engine?  Or a new problem?   Have you ever seen it work correctly?

It sounds like your X3 connector Pin #3 does not have continuity with the battery.  Open Fuse?
Confirm that BOTH Backup-Power and Start-Power are OFF after starting.

If nothing else ...  Connect and run the BUDS set on a running engine.
Monitor the "Main Gauges", "Health", and "Internal and GSM" tabs for any anomalies.

I’m encountering a similar issue recently. Started the engine, added power to 2,500 rpm and still shows battery voltage around 12.5V (a little higher than what you had 11.5)

The engine also quit on me couple times, feels like there’s something going on with the supply power.

No indications of generator failure or whatsoever. Still trying to figure out what happened.

I wondered if you figured out your situation since I am having the similar symptoms…

It turned out to be a burnt out Stator/Alternator. Not sure what

caused it, I am only pulling 6Amps from Regulator B. The engine has

done ~1400 hrs. The problem of the engine stopping was caused by

Reg.B not working. When the engine starts it's running off the Battery,

the engine then starts Gen.B runs the ECU until the engine

Revs are high enough to kick in Reg.A which then takes over

running the ECU. The problem is when Gen.B isn't working

the engine stops when the battery is switched out of circuit,

which happens automatically after 30secs. 

In normal operation, with both alternators functioning, when the engine starts alternator B powers the engine systems for a few seconds until alternator A takes over.  But depending on how you operate your start power switch, an alternator B failure will show up in different ways.  

Assuming alternator or regulator B has failed, a couple different things may happen when starting the engine.

1. If your battery is still charged, then with the start switch ON the engine is able to start and run on the battery (only) until it makes the switch to alternator A. You may not even notice a problem, except lower battery voltage and a discharge of the airframe electrical bus. If unnoticed, eventually the battery will discharge and the airframe power will fail.  

 2. If after starting the engine you turn off your start power switch quickly (before the engine has switched to alternator A, then the engine will stop because you have disconnected the battery which was supporting engine operation (normally supported by Alternator B during this period).  

Once the engine is running on alternator A, AND you have turned off the start power switch, then nothing you do with the airframe electrical system will affect the engine. This is because it’s running on a fully isolated electrical system powered by alternator A. The engine won’t care that alternator B is dead, and your only indication of a problem will be low voltage and discharge of the airframe electrical bus.  However, if you leave the start power (or backup power) switch on, this keeps the engine and airframe electrical systems connected and operating as one.  This can be a good thing if both Alternator A and B fail and you want to tie in your battery to keep the engine running as long as possible.  But if only alternator B has failed, and the battery is already low, then turning on the backup power switch or the start power switch can inhibit the engine operation.  This is because Alternator A is right-sized for the engine loads, but won’t keep up with the airframe loads. Connecting the compromised airframe electrical system to the engine electrical system may essentially overload it and draw the voltage down to a point the engine will stop.  This is exactly why the systems are fully isolated - to avoid this.  

If your battery is not charging, there is likely a problem with alternator B, or regulator B, or the connection from the regulator to the airframe power buss.  The test procedure for the stator and regulator is easily performed and conclusive.  Rotax has seen problems with the B stator.  There have been service bulletins to replace the stator, and more recently a new oil spray nozzle was introduced to keep the B stator cooler.  Unfortunately this upgrade requires that you replace the starter sprag housing and the ignition housing.