** This solution will not work for ChipScope Analyzer 11.2-12.1. The issue is resolved in ChipScope Pro Analyzer 12.2.
What is happening is that the ChipScope Pro Analyzer tries to access all USER instructions for the targeted device when polling for ChipScope Pro Analyzer cores. This means that if you have a ChipScope Pro Analyzer core plus some custom logic utilizing the BSCAN primitives, ChipScope Pro Analyzer toggles the state of your custom logic BSCAN primitive.
Edit a ChipScope Pro Analyzer project file (.cpj) and add nab avoidUserRegDeviceX property (where X is the device index, e.g., 0 for the first device in the chain, 1 for the second, etc.).
The following example avoids scanning USER register 1, 2 and 3 on the first device in the JTAG chain:
The example below avoids scanning USER register 1 on the second device in the JTAG chain:
Read in the .cpj project file to the analyzer before opening the cable. When the analyzer scans the JTAG chain, it will report in the log panel that certain user chains have been skipped according to the property settings.