Only 2 of the other speakers can have an assignment that would result in them only being active in association with the second audio zone. All the other speakers are and will be assigned to the main room. If what you say is the case then I'd suggest you go start from scratch, rewire the speakers and cnfigure the receiver again as though you'd just got it. This will not only resolve the issue you are having, but also give you a better understanding of how the assignments work relative to the speakers present.
If your intent is a 5.1.4 setup then you need the following setup and configurations:
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- Set the ASSIGN MODE in the AMP ASSIGMENTS to 9.1ch
- Set FLOOR LAYOUT to 5ch
- Set HEIGHT SP to 4ch
*NOTE If using upward firing as opposed to HEIGHT or CEILING speakers then use the DOLBY SP setting as opposed to the HEIGHT SP setting.
Once this is done then run the Audyssey calibration.
After the calibration is complete then you can address the bass management configurations.