i never had a 939 machine, but i remember seeing that problem in some s462 motherboards, also in some 775 too
still, i think that since socket 754 up to fm2+ they all can use the same heatsink, my main machine is AM3+ with the stock cooler and does present a little bit of curvature
if you can't find a solution, i suggest that you can try a newer heatsink to see if the warping is still pressent

some s462 motherboards

S462 cooler can't warp the board, because it's connected only to socket. Boards with mounting holes for water cooling solutions and air supercoolers is different story.

And can anyone recommend a 939 cooler that is less likely to warp the board so much? Preferably without that stupid lever

Any cooler with its own backplate like Thermalright 128SE.

but I'm not really comfortable leaving these heatsinks on, especially after going through the whole re-capping effort

There shouldn't be any problem, PCB can handle prolonged warping. I've been using Thermaltake Big Typhoon VX (no backplate) on LGA775 boards without any problem for many years.
What any PCB can't handle well is regular bend/unbend cycle, hence all those scary stories about Aplle smartphones.

TheMobRules wrote:

The metal plate that goes in the back is supposed to prevent this, but it seems to be doing nothing...

Are you sure it is installed correctly?

Board warpage is something that has concerned me ever since I first saw a CPU cooler that attached to the PCB instead of the CPU socket. For two Socket AM2 systems I use Thermaltake coolers which I modified by filing the locking lever to reduce the clamping force. There's no need for it to press down very hard on the CPU.

The backing plate can only do so much, often when removing one from an old board it is also warped.

The Serpent Rider wrote:

There shouldn't be any problem, PCB can handle prolonged warping. I've been using Thermaltake Big Typhoon VX (no backplate) on LGA775 boards without any problem for many years.
What any PCB can't handle well is regular bend/unbend cycle, hence all those scary stories about Aplle smartphones.

Interesting, thanks for the info! I wasn't sure about the how well these boards tolerate being bent.

derSammler wrote:

Are you sure it is installed correctly?

I attach the metal clips to the tabs on the black retention frame, and then push down the black lever on the heatsink until it latches. Is there anything else to it? At least that's how I remember doing it back then.

In any case, pushing the lever seems to exert a huge amount of pressure on the black plastic frame around the CPU socket, the frame deforms to the point where it also bends the backplate that is screwed to it, and the board along with it. So it seems the bending is caused by this tension rather than the weight of the heatsink itself. This is why the board gets bent "upwards" near the CPU rather than "downwards" like when it's caused by heavy coolers. I'll try to post some pictures tomorrow.

Maybe a sturdier backplate could help, the one I have is made of metal but seems to bend easily.

Board bending is not limited to socket 939.
Backplates (if present at all) do not always help, as the distance board-case varies.
Placing felt pads of suitable thickness under the socket often helped me to keep things straight, avoiding warping.