I am not familer with RAppID, but probably you selected local counter bus (BSL=1) for individual eMIOS channels and channels that serve counter bus B (ch0), C(ch8) and D(ch16) do not enable prescaler and are not set for MCB mode.
Try to select counter bus A (BSL=0) for individual input channels and confige ch23 to serve counter bus A, set it for MCB mode.
I am not familer with RAppID, but probably you selected local counter bus (BSL=1) for individual eMIOS channels and channels that serve counter bus B (ch0), C(ch8) and D(ch16) do not enable prescaler and are not set for MCB mode.
Try to select counter bus A (BSL=0) for individual input channels and confige ch23 to serve counter bus A, set it for MCB mode.