Well, SQ takes one to two days for crediting miles. Normally my miles for my inward journey post before I take the return flight. Do confirm your Boarding Pass had your SQ Krisflyer number printed on it - missing FF numbers is usually a clue that the system did not capture this.

If you did present your Virgin card and the flights were all code shares (had a SQ and Virgin number) you should get CO miles for all sectors. If they were SQ operated flights only - you can try for a retroactive mileage claim to Krisflyer - though this might take a while... would help if you have boarding passes on hand.