I forgot to post this quite a while back, but I should have. I'm surprised that I haven't heard this mentioned anywhere else, but I had a similar problem that took a little time to figure out.
Backstory -- When I first started putting together my first mining rigs, I noticed that some cards were performing slightly better than others. Card performance varied anywhere from 1 to 4 percent. It didn't make any sense. I had 32 identical cards that had the same clock rates, so the performance should be nearly identical between cards. At the time, I was using separate instances of Phoenix for each card instead of a combined miner, so I could see the hash rate discrepancies.
Long story short, I noticed that the cards connected directly to the board never varied... only the cards with 1x risers did. My rigs have 4 cards each -- 2 in the board and 2 connected with risers. I then noticed that the hash rate in Phoenix would fluctuate when I moved the riser cable around. Yep... the risers easily pick up EMI from nearby components.
Since PCI Express runs at such a high frequency, it's extremely susceptible to interference over long distances. You'll notice that most of the "name brand" risers are shielded (like this one http://www.newegg.com/Product/Product.aspx?Item=N82E16815158290
). They're shielded for a reason.
With every miner I assembled, I sat and watched Phoenix while moving the cable around until I hit the max hash rate (and then left them there). However, I had cards that would stop mining randomly. Sometimes they would mine for a few hours, sometimes 1/2 of a day, and sometimes days without hanging. When they would hang, it didn't take anything more than restarting the miner.
I started logging these hangs over the course of a week or so. I noted which machines would hang and which cards it happened to. Of course, it always happened to the cards with the risers.
Here's what I did to fix it. I bought a roll of aluminum duct tape and shielded the cables myself. Be very careful with this though -- aluminum is very conductive. If you're afraid of them touching against your components *wrap them in electrical tape* after applying the aluminum tape. I'm sure you could use aluminum foil to shield them too, but I'd recommend the tape if you have very many risers to wrap.
After doing this, I *rarely* get a miner that hangs. With 54 video cards mining 24/7, I only have to restart a miner about once every week or two. It rarely happens. Here's the exact tape that I used, but I'm sure that just about any aluminum foil will do the job. http://www.amazon.com/Nashua-324A-Cold-Weather-Premium/dp/B0015V93KG
. I bought it at Home Depot.