As the title stats, past few days i've noticed a slight "clicking" sound coming from my card at low fan speeds/idle. Using X1 to monitor fan speeds I noticed that Fan 3 doesn't hold its RPM while using the same fan profiles as fans 1 and 2. For example, fans 1 and 2 are holding a steady 11%RPM while fan 3 jumps between 13-21%. This card has the most recent firmware (day one card that had fan controller beep issue). Anyone else notice something along these lines with their card?

Unfortunately the beta did not solve the issue. Through some more trouble shooting I have verified that the clicking issue is definitely coming from the #3 fan when it is ran isolated in X1. Starting with #3 fan at 0 RPM the clicking sound and sporadic RPMs persists until roughly 650-700RPM. Once the RPM reaches this level the fan RPM excursions (ranging from 50-100RPM either direction) go away and the RPM stabilizes as well as the clicking sound stops. If you slowly drop the RPM back down the sporadic RPMs come back at 10%. Neither fans #1 nor #2 have this problem. Both of those fans can hold rpm from 0%-100% with issues.
 
Also adding that running this same test sequence manually with all the fans linked all fans are at the same RPM down until 10%. At 10% (300RPM) fan number three's RPM falls off to 30-180RPM, while fans 1 &2 maintain 300 RPM, and the clicking sound starts (assuming its probably the fan controller making the clicking sound?).

Randomly the number three fan doesn’t even show up in X1 unless you restart the computer. I’m hoping this is just a software issue and not a reason to RA the card.

Okay so i'm gonna be guessing here but what seems to be the case is the same as normal case fans would react : they can't get below a % too low because they won't receive enough current. For example I have a bunch of 3000rpm corsair fans, if I try to get them below 40% (so that would be around 1250rpm) the fans just stop. Depending on the %, the fan might try to spin then fail or do it but at some point stop. 
 
I don't know how the fans are plugged but my theory is that the first 2 receive "enough" current to be able to sustain " lower than average " operations, while the 3rd fan just don't get enough juice to be that low and the clicks you are hearing is the fan trying to spin but not enough current goes to him so he spins a bit, slows down, clicks, then gets back up a bit, etc. To me, it seems you should raise a bit the fan speed of #1 and #2 and try to see if this solves the issue. 

I know this might not be the best in term of noise but sadly fans very very very low speed when they can get up to 3000rpm can have issues or not function at all. 
 
 

I'm also having similar issues with fan 3, it takes longer to speed up and slow down compared to fans 1/2. Also noticed that if the pc goes to sleep, when it wakes up fan 3 will stop responding altogether. X1 sees it and I can bump up the fan% but RPM stays at 0.

Actually I just installed X1 v1.1.0.9 and so far have not been able to replicate my issue with Fan3 not turning on, however it still is slower to respond.
 
Edit: actually looks like FAN3 rpm is tied to fan2 rpm. if I just adjust fan3 there is no change