It seems there was EnsureAPI=Tru in the .ini, corrected it, hmh. o_O The .conf files were okay.

With this same version at least, keeping cgwatcher open, starting the miner, stopping it, starting it again doesn't fix the mapping.

Current contents of my .ini:

[CGWatcher]
UseBackupHardwareMode=False
CurrentProfile=1
[Settings]
MaxAvailableLogEntries=100
Autorun=False
Autolaunch=False
MinimizeToTray=False
StartMinimized=False
NoPromptOnExit=False
PosScreen=0
PosX=13
PosY=435
[Miner]
ProcessStartCushionSeconds=15
ProcessID=0
ProfileID=1
MyProcessID=0
WindowMode=0
Address=127.0.0.1
OverrideAPIPort=False
Port=4028
GPUCount=3
[Monitor]
MonitorOn=True
Interval=5
EnableOverheatProtection=True
NotRespondingRestartChecks=3
AllowDisableWERUI=True
ForceCloseProgramsOnRestart=False
HashRateType=1
HashRateCounter=3
RestartGracePeriod=180
HoursRestartValue=24
CheckShareCountMinutes=10
HashRateRestart=False
HashRateCutoff=800
CheckShareCount=False
AutoRestart=False
SickDeadGPURestartType=0
PrivilegeLoss=False
EnsureStaysRunning=False
[System]
GPUCount=2
CPUCount=1
[Config]
EnsureAPI=True
[GPU-Map]
0=1
1=2

Dunno how that Tru value got there, I don't edit the .ini file directly, nor have ever I typed a True or False value manually in any field, as far as I can recall at least. But it's fixed for now and will not where to look if it happens again.

So, go ahead and update the file, and I'll see how the mapping goes.