I was hoping my findings could help someone else developing idle diagnostics: I found that idle diagnostics were failing when using the microcode provided with the AN12336SW with the FRDMPT2001EVM development board.
The following lines were generating software interrupts:
jocr idle_diag_fail0 _sc2v;
jocr idle_diag_fail0 _sc1s;
jocr idle_diag_fail0 _sc3s;
The interrupt was being thrown before the voltages at S_HSx and D_LSx had sufficient time to reach their stable value.
In order to give the PT2001 enough time for the capacitor to charge at S_HSx and D_LSx, I moved the "bias all on" function into the INIT PHASE of the microcode and now it successfully passes all idle tests.