As I understand it, when the screen says only Dolby Digital , the 990 is simlpy decoding the information from the DVD. When it says Pro logic II, it is processing the signal to matrix out the various channels. You can always get to Pro Logic II by toggeling the Dolby Modes button on the 990 remote.
That's pretty much it. Dolby Digital will record the sound on discrete tracks. For example 5.1 sound is recorded on 6 tracks. You can also record the 5.1 sound on as few as 2 tracks which is called matrixing. The Pro Logic II will decode these matrix channels and output the 5.1 (6 channel) sound. Pro Logic II can also take in stereo sound and process it up to 5.1 output. I believe the 990 will select the decoder based on the format recorded on the disk.
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