The alarm you noted is related to the encoder and generally means that it is failing. Running at 50% usually confirms this to me.

If this has indeed been happening since new then it may possibly be parameters. Have your HFO verify your parameters for you or provide you with the proper ones for your rotary.

Not trying to be a jerk, but why have you been running like this for almost 12 years now? This should have been addressed under warranty.