When I use the Pause-IR or Pause-DR functionality in an XCF00P device, Boundary Scan (JTAG) tests fail. (The Pause-IR or Pause-DR state is used when a pause is needed while data is shifted into the instruction or data register.)
If the TAP is returned to the Shift-IR or Shift-DR state after a temporary pause in the Pause-IR or Pause-DR state, the contents of the shift register are corrupted because the shift register incorrectly recaptures its initial values.
To work around this problem, do not use the Pause-IR or Pause-DR state when scanning the instruction or data register. If a pause is required, TCK should be halted (this is often referred to as a "gated" TCK).
This issue is documented in the Platform Flash Data Sheet in the IEEE 1149.1 Boundary Scan (JTAG) section.