Many discs include both Dolby Digital (5.1) and ProLogic track. While the Sony advertises auto soundtrack selection, this does not work on some discs (notably those from Paramount). Using the display of your DVD player, see how many channels are being played on one of your troublesome discs. It's probably showing 2/0.0. When you change to the proper 5.1 track it will show 3/2.1 and your receiver will of course detect it as 5.1.

Just as a side note, technically *ALL* audio on DVDs is encoded in Dolby Digital - whether it is mono (1 channel), stereo (2 channels) or full surround (6 channels).