Here's something to keep in mind: not all HD material broadcasts in Dolby Digital 5.1. In fact, a surprisingly large amount of it broadcasts in Dolby Digital 2.0 - plain old stereo, just using Dolby Digital encoding. The 990 treats these two as distinctly different entities and remembers different decoding modes for them.

If the display only says "Dolby Pro Logic," then it is applying Pro Logic processing to a Dolby 2.0 signal. Applying Pro Logic to a 5.1 signal would require 7.1 speakers and would show up as "Dolby Digital+Pro Logic IIx." Based on that, it sounds to me like the 990 is doing what it should: decoding Dolby 5.1 as it should (with no additional processing) and applying additional processing to Dolby 2.0 (likely based on the "default mode" specified in the input menu).

Here's a trick I use to tell Dolby 5.1 sources from Dolby 2.0 sources. The front panel of the 990 has separate indicator lights for "SUB" and "LFE" near the bottom middle of the speaker cluster on the left. If the LFE indicator is lit up, then I've got a ".1" signal. If it isn't lit up, then I've got a ".0" signal that is probably only 2.0.