Sub Not Waking Up

I have a Yamaha CX5100 Receiver and two Sunfire HRS8 subs.  I moved my equipment around in my cabinet, got a new am to power my R/L, and new R/L speakers.  I am still using the same center, rear, and 7.1 channel amp to power the others.  

My problem is my subs will not turn on.  I ran the Yamaha YPAO and sound came from them and it configured them at 2.5.  But after they will not work.  I think they are going in standby and not getting a signal to turn on but for the life of me I cannot figure out why.  

I have another Velodyne sub in another room and it works fine and the Sunfires work fine in the other system.  It is just the sunfires with the Yamaha.

Any suggestions would be appreciated.

I'm not familiar with that particular receiver or those subs, but with most receivers, there are ways to activate or deactivate the subs and also the listening mode you've selected may affect whether the subs are active or not.  Double check all that.  Worst case, just leave the subs turned on.

"I rewired them using the speaker level inputs coming straight from the amp."

Try using a regular subwoofer cable and see if they are triggered then.

I know this may seem elementary, but do your subs have gain control? Make sure they are turned-up if so.

Using YPAO in the receiver itself sets volume/gain within the receiver, yes, but some have found if the gain is not turned-up at the sub itself there could be an issue with it triggering on at ‘start-up’ volumes, or, not enough initial gain to trigger it. Once the volume is adequately turned up at the sub itself, then adjust via YPAO, or within the set-up settings. Personally I have never found the YPAO settings to be adequate for correct sub settings via LFE when I used to run my sub that way. I always manually adjusted its gain within the receiver settings with a meter.

I know this may seem elementary, but do your subs have gain control? Make sure they are turned-up if so.
Or use a 12V trigger outlet for the subwoofers.

most probable problem:
a)You probably have the volume control knob on the sub way up.
b) YPAO may have compensated when it does it's level matching with your speakers by turning the level way down for the sub. The signal the receiver sends now is insufficient to "wake up" your specific sub during playback.

Start turning down the volume knob on the subwoofer unit such that YPAO is setting sub levels to +3dB or more when it does its level matching. The receiver should send something big enough/sufficient to "wake up" your sub. 
Actually YPAO is notorious for setting the sub level via LFE too low regardless of the gain setting at the sub, which as I said, thus I always adjusted it manually when using LFE with my receiver. Albeit I don’t do that anymore.

But yes, as I also said, most probably the sub gain is set too low.
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