John, I decided to copy the information related to LFE from the RX-Z9 instruction manual below so if you have questions we can always refer back to this post.
Page 62
LFE Level – Adjust the output level of the LFE channel for Dolby Digital or DTS signals.
Page 70
LFE Level (Low-frequency effect level)
Use to adjust the output level of the LFE channel according to the capacity of your subwoofer or headphones. The LFE channel carries low-frequency special effects which are only added to certain scenes. This setting is effective only when this unit decodes Dolby Digital or DTS signals.
Page 74
Front (Front speakers)
Choices: Large, Small
· Select Large if you have large front speakers. The unit directs the entire range of the front left and right channel signals to the front left and right speakers.
· Select Small if you have small front speakers. The unit directs the low-frequency signals of the front channel to the speakers selected with “Bass Out”.
Bass Out – LFE signals carry low-frequency effects when this unit decodes Dolby Digital or DTS signals. These low-frequency signals can be directed to both front left and right speakers, and to the subwoofer (which can be used for both stereo reproduction and sound field programs).
Choices: Both, SWFR, Front
· Select Both to direct LFE signals to the subwoofer. Front L/R low-frequency signals are directed to both the subwoofer and front channels, and all other low-frequency signals are directed in accordance with other speaker settings.
· Select SWFR if you connected a subwoofer. The unit directs all LFE and low-frequency signals in accordance with other speaker settings.
· Select Front if you have not connected a subwoofer. The unit directs all low-frequency and LFE signals to the front speakers (even if you have previously set Front to Small in Speaker Set).
It looks like you have everything set up right, but if you still have doubt about something may be wrong, you can try resetting the processor to factory default condition and then run YPAO again, following the instructions on Page 33-34.
After that, double check to make sure:
- All speakers are set to "Small", so that the low-frequencies of the front, centre, and surround speakers will be directed to (in other words, added to) the LFE out.
- Crossovers for the front, centre, and surrounds are set to 80 Hz.
- Bass out set to SWFR.
- LFE level set to default "0" (I am assuming the default setting is 0 but you can confirm that as you have the AVR and I don't).
- Check the speaker levels (see Page 76) and let us know what YPAO set them to, including the subwoofer level (again, this is not the same as the LFE level).
Resetting to default condition could possibly fix minor corrupted software but if you are happy with the way the unit is behaving and everything sounds good, then you should just relax and enjoy. The RX-Z9 is (or I should say "was") indeed a very high quality flag ship Yamaha unit.
Edit: You should also double check to make sure your L & R channels are in phase, that is, + to + and - to - at both the AVR speaker output terminals to the speaker input terminals. Normally YPAO should be able to detect whether they are in phase or not but you never know, only take a few minutes to check things out.