The cinema DSP modes (Hall, etc.) typically only work with a stereo signal - specifically PCM stereo or analog stereo.

If the signal is Dolby Digital 2.0, the Dolby decoder kicks in and because of the way the processing takes place those modes often cannot be used. (As an example, the Model 1070/970's 5 Stereo mode only works with PCM stereo or analog stereo sources - and not with Dolby 2.0. The 990 may behave the same - I don't recall and didn't see it mentioned in a brief glance at the manual.) You should still be able to engage Pro Logic II/IIx with Dolby 2.0 sources, though.

If the signal is Dolby Digital 5.1, then all of those modes are meaningless (there's already center and surround data, which erases the purpose of those modes). The only matrix processing modes that will work with Dolby 5.1 are Dolby EX (which was created specifically to expand 5.1 to 6.1) and Pro Logic IIx (which expands the capabilities of Pro Logic II to seven channels and can thus be used with 5.1 sources to expand them to 7.1). Since you have a 5.1 speaker setup, none of that really matters anyway and we can simply say that Dolby 5.1 stands on its own.