An addendum to my Upsample comment (taking a break from work and a few chores): it does also work with Dolby EX and DTS ES when the bitstream contains flags that call for those modes.

From all I've ever read, Pro Logic IIx should be identical to Pro Logic II except for the presence of the two surround back speakers - technically, PLIIx is an extension of PLII that uses the same matrix decoding but adds an additional step to produce discrete surround back channels. I would be surprised to find a significant difference in sound unless you are talking about the effect produced by the additional speakers (which may in fact be what you are talking about, in which case I would agree that there will be definite differences).

Does the Boston allow you to select either Pro Logic IIx or Pro Logic II processing when surround back speakers are enabled?

Two more tests before I go back to my plans. First, a Dolby Digital 2.0 source. The options offered by toggling through the Dolby mode button are Dolby Digital+Dolby VS 5-SP Wide (which is a five-channel mode), Pro Logic IIx Movie, and Pro Logic IIx Music. Stereo mode button options are Stereo and Upsample. Second, a PCM stereo source. The options for Dolby mode button are Pro Logic IIx Movie, Pro Logic IIx Music, and Pro Logic II Movie+Dolby VS 5-SP Wide (a five-channel mode that I've never messed with). Stereo mode options are stereo, bypass, upsample, 7-stereo, and 5-stereo. DTS mode button options are DTS NEO:6 Music and DTS NEO:6 Cinema. From all that I've done with the 990, I've found that the 990 will remember any one of these modes for a specific signal format on a specific input - telling it to apply Dolby VS 5-SP Wide (which the manual says can be "used to expand the soundfield when front left and right speakers are positioned close to TV") to a Dolby 2.0 source on the VIDEO1 input will not affect how it processes Dolby 2.0 sources on the DVD input. A specific example (again from my normal mode of operation): PCM Stereo on the CD input is processed in Upsample mode, but PCM stereo on the Cable input is processed Pro Logic IIx-Movie. It sounds like this is not the case with the BA receiver - a condition that would drive me just a bit nuts since I like using Pro Logic IIx processing for PCM sources from my HD cable box but not from my CD's. That there are differences in this sort of behavior is not terribly shocking: the 990 shares the core hardware with the Sherwood platform that the BA is built on, but I don't think much of the Sherwood firmware was re-used for the 990. After all, the menu structure and bass management are both substantially different, and there's no telling what differences lie deeper under the hood.