I had this issue with VA (and yes, I know this is a QF thread) when they formed a partnership with, and later took over, Skywest Airlines in WA. There were all the promotional blurb about how you'd be able to earn SCs and points with Skywest flights etc etc, so we found it was handy to use the short return hop down to Busselton as a status run. However every time we did, although the flight was actually booked as a codeshare through the VA website, they posted as ineligible flights - so it would be back on the phone to VA/Velocity who would argue with me that these were charter flights and therefore not eligible, which was absolute rubbish. Each time we eventually ended up getting the SCs and points, but it usually took weeks and multiple phone calls to make it happen. In desperation, I even had to get Skywest involved a couple of times to prove the flights were scheduled codeshares with VA.