It happened to me with the most expensive part of my recent holiday: 2 Club rooms for 4 nights in the Anchorage CP, both posted as non-qualifying. As it was worth over 30,000 points I was a bit perturbed.

To my surprise within 15 minutes of emailing IHG the points had been manually posted!

(I didn't need to give them my invoice, just the original booking number was enough. The reservation had been booked through IHG's website on the best flex rate and had been manually split into two by the CP. The invoices said something like "corporate rate 6" on them, although in total they were for the correct amount).