The 990 does not have analog bass management on the 7.1 input; the 950, 1070, and 970 have an option for an 80Hz analog crossover on the 5.1 or 7.1 input. A stereo analog input can get bass management with any of the above units.

The 990 absolutely should be able to provide you with all the bass management you need for a passive sub (I'll paste in some notes about the 990's bass management below, borrowed from my 990 review). The way things changed when a center was added sounds like a quirk/bug that I would suggest giving Outlaw a call about. With the center on, can you turn the surrounds off? If so, what does the sub do?

990 Bass Management Options:

• Digital Bass Management: This covers most sources, including any digital input and any stereo analog input that is not set to "bypass." These sources are processed exactly as you would expect. Small speakers have their signals rounted through the high pass and low pass crossovers as defined in the "SPEAKER X-OVER" menu, with the low frequency data redirected to the subwoofer. In the event that the subwoofer is disabled, the mains must be set to "large" and will receive the LFE channel and any redirected bass. Additionally, tone control and speaker time delays are applied by the DSP along with any requested or required surround mode processing.
• Bypass Mode with analog input: The 990 retains the ability to provide a bypass of all digital processing for stereo analog inputs. In this mode, the 990 skips all digital processing and passes the left and right signals directly through volume control and on to the amps. In a bit of homage to the Model 950, perhaps, the analog bypass offers bass management that behaves similarly to the 950's. The full range analog signals are sent to the speakers without alteration, and if the mains are set to "small" a copy of the signals is converted to digital and processed through the bass management to produce a subwoofer signal. As with the 950, if the mains are set to "large" the sub is not used. Because the DSP section is bypassed, tone control and time delay are not applied in either case.
• Bypass Mode with digital input: The "bypass" option is available for both analog and digital inputs, which at first glance struck me as odd. When bypass is used with a digital input, only the digital bass management is applied (high and low pass crossovers, if the mains are set to "small"). Tone control is bypassed, as is (obviously) any surround mode processing.
• 7.1 Direct analog input: Three years ago, the Model 950 offered a unique feature in its multichannel analog bass management. It had a switch that would enable or disable an 80Hz high pass filter on all five full range channel; a permanent low pass filter in each channel routed low frequency data to the subwoofer. The Model 1070 receiver has been shown to possess a similar switch, although full details on how that switch will behave are not yet available. The Model 990 lacks such a switch, opting instead for a different approach. By default, it converts the data to digital and applies the full digital bass management settings. If all speakers are set to large, no bass management is applied and the signals are left in the analog domain all the way through the unit. Either way, the DSP section is bypassed (similar to the bypass mode for digital inputs), resulting in tone control and time delay not being applied.