The problem I encountered last year with two stays, one a Great Rates and the other a Corporate Rate [against which I had always until then received points] seemed to come from the fact that the check-in agents at both properties miscoded my rate so it appeared on the check-out folio as a Travel Industry rate, rather than the one it was booked at. I received all my stay benefits, but it took months of faxes to finally get the appropriate credits fro PC.
The explanation in the above posts is correct: all rates booked on the PC site, except for Entertainment Book rates, qualify for points. However, I don't believe any third party bookings [expedia, tavelocity, priceline] now qualify unless these are at rack or negotiated corporate rates.
And the IC Cali should have given credit for the paid night of the two night certificate stay. I have never had one of these discounted, and they show as 2 nights credit, not just the single paid night.