I would like to know how the XDS110 handles default registers.

I am seeing strange behavior on a TMS32028F279S and XDS110

At times, this processor is not properly responding to the analog comparator input COMPIN1. The problem is a rare event, but we have evidence that this is happening. We ran experiments to try to understand the issue. We did a "clean" and "rebuild". Loaded the new .out file, and the problem was gone. Then we went back a loaded the .out file that caused the problem. Again, no sign of the problem. We did this on a second unit that showed the problem, and again, merely reprogramming is solved the issue.

This leads me to believe that the code is not defective, but somehow a register involved with setting or connecting the comparator to the PWM became corrupted. For many of the settings, the default value is appropriate, so we do not set them in code. I mention this because my theory is that one of these registers are getting corrupted, and re-programing solves the issue.

I would like to have any and all documentation that exists on the XDS110. I would like to understand how these peripheral settings registers are effected during the erase and Flash process. 

I would like to know if someone else reported a similar problem. This issue has full visibility of several management chains. There are delivered units currently considered at risk.