I've found this situation is a bit hit and miss when the carrier concerned is not a Star Alliance member. Two examples are AirOne in Italy, which has a codeshare arrangement with LH, and Great Lakes Aviation, serving numerous small towns out of Denver, which has codeshares with UA. When LH or UA have issued a bording pass for a connecting flight on AirOne or Great Lakes, I have been credited with miles for the flight even though its not on LH or UA metal. However, on the return checking in with AirOne or Great Lakes and getting one of their boarding passes, I have never got miles. On one occassion I posted in an AirOne boardng pass with an LH flight number clearly shown but was politely told the flight did not qualify, even though my account showed I had received miles for the flight on the same carrier in the opposite direction. The only lesson I can share is, always try to get a connecting boarding pass from a Star Alliance carrier, as then you will improve your chances. Of course this won't always be possible.