When you get a DD signal, the 990 has to apply Dolby Digital. When it shows Pro Logic on the front panel in those cases, it is applying Pro Logic in addition to Dolby Digital to achieve either 5.1 or 7.1 (Once the planned firmware update arrives, we'll hopefully have a way to push a button on the remote and display the current mode, but for now the most surefire way is to hit the "SURR MODE" button on the front panel.)

I've not had any trouble with this with my unit, but it may be due to a combination of personal preference and some two-channel setup. My DVD and cable sources have all been "taught" to use my preferred method of getting 7.1 sound: DD 2.0 through 5.1 use a combination of Dolby Digital and Pro Logic IIx-C to get 7.1, DTS 5.1 uses DTS+PLIIx-C (I've also used DTS+Neo:6, which is what used to be called DTS-ES Discrete), and PCM sources use Pro Logic IIx-C. My two-channel listening is done with the same source device (typically my Yamaha DVD player, but sometimes the OPPO as well) through an audio source configured to use upsampling with PCM stereo inputs. This saves me from having to switch back and forth from upsample to PLIIx for PCM sources (on the rare instances where I get a video disc with PCM audio on it).