I've just taken delivery of my AQ5 and a couple of PA2s, and I have this exact issue too. This is after a fresh install of the software, I can connect to everything over usb no problem, but the two PA2s don't communicate at all over AquaBus They came with latest firmware too....

McGreggor - Did you remember to change the aquabus channels when you hook the PA2s to the usb? They can be anywhere from 50-57. Each one has to be different. Do you have any thing else connected to the aquaero?

Yes I've changed the aquabus channel number on the one PA2 that's responding via usb connections, and after an hour trying, I have got one of my PA2s now connecting over AquaBus. Only problem is my other one doesn't respond even to USB connections, it just blinks all the time and USB device not recognised which I'm reading about on other threads might mean an RMA.

Are your PA2's Ultra's or Standard?
I have a new PA2 Standard that failed quickly. My older PA2 Ultra's are still kicking along nicely.

I've got Ultras running 1006 FW. I've been bench testing on and off all day today... and my other PA2 (that has been working) has just started to behave in the same way... It's blinking fast and the fans aren't powering on. I just connected via USB, and only the system tab appears in AquaSuite, and no firmware version is recognised! I previously saw the other tabs and had control of the attached fan etc. Interestingly, when this first happened, I had the PA2 attached via AquaBus, and AquaSuite still had an entry for Fan5. It was showing that 12v was being output by the PA2, but the Fan RPM was 0 (as the fan wasn't moving).

This is very worrying, my intentions are to have the PA2s in my garage to run pumps and fans, so I won't be able to see the fast blinking should it happen after install, and as the fan i'm testing with stays off, this could result in an overheated PC

Pretty much the same thing here, although it was my Standard version that quit on me out of the blue. Powered up one day and the fans weren't running.
Like I say, my two Ultra's I've had for a while are working fine, for now anyway.

I don't think there is a way to reset the PA2's, other than flashing firmware, which mine seemed not to accept.

I also had the pwm function of Fan 4 go out. This appeared to happen simultaneously with one of my MCP35x pumps dying. Since the pump was only connected to the header with the rpm and pwm wires, I'm not real sure what to make of it, and neither is Swiftech whom I contacted for RMA of the dead pump.
First pwm control went out, and the fan header displayed maximum rpm's. Eventually even the rpm quit showing as the pump finally died. Since this was dual pumps with a single top I separated them and thankfully the other pump is working fine, although now it's just running wide open all the time since it's no longer plugged into the Aquaero. (My motherboard headers run the pump either too slow or wide open so I don't bother with it).
All of this is what you would expect with the pump failing, of course, but the question is what caused what.
Did the Aquaero fail and damage the pump, or the pump failed and damaged the pwm circuit on the Aquaero? I have no idea, beyond my pay grade.
I have another Pro unit coming today so I can get back to pwm control of my pumps.

Yeh, neither of mine are responding to further firmware flashes. There seem to be pinouts on the side of the PCB of the PA2s, which must be how they are initially programmed I'm guessing. Would be nice if the hardware/software was made available to re-program the PA2s for this situation, I can't believe anything is physically wrong with the devices, its just got itself into a pickle.

I'll be logging with support if I can't get them working again tomorrow, see if they have any ideas.

Once I again I have the "missing" PA2's.

Can connect to PA2 via USB and all is fine, Aquabus connection shows nothing. Swapping Aquabus cables didn't help.

Fixed. Turns out I had two bad aquabus cables. Must have been damaged from R&R so many times.