I recently developed an annoying brake rub when climbing hard while standing out of the saddle. It is not continuous but occurs with every downstroke on the pedal. I have a carbon frame and I am wondering if I am flexing the frame so much that it is causing the rub? (Or am I flexing the wheel?) Any adjustment I can make to resolve it?

yes, your flexing either or both the wheel and frame. It's normal, especially when standing and counter leaning the frame for power.

There's no magic cure, but start by aligning the wheels as well as possible, making sure they're tight and true and have minimum (zero) bearing play. Then center the brakes perfectly, and finally, adjust them to clear when you stand, assuming of course, that you have enough lever travel.

You can also practice a smoother style, but it's better to make the bike adjustments than make yourself crazy.

Assuming the brakes are set with a small gap to the rim, you can buy yourself some relief by opening up the shoe-to-rim clearance a bit. I had a bike that did what you are describing and the fix was to set the brakes with a bit more clearance.

what wheels do you have?

Make sure spoke tension is up to spec, or switch to wheels with more/stiffer spokes. Can you operate the release on the rear brakes before you start the climb.

+1, Ensure spoke tension is adequate and learn to loosen the brake release.

I had the same issue and just broke down and bought new wheels. I had the Mavik Aksyums (sp) and am upgrading to CK R45 hubs and DT-Swiss 585 rims (32 spoke in the back and 28 in the front).. My first set of hand made wheels. I'll keep you posted as to when I get them. I assume they will be stiff enough considering the high spoke count and depth of the rims. The only downfall is that they are relatively heavy (and maybe a bit rough over bumps).. but I'm not a racer and would rather be able to stand up and pedal than have a feather weight bike.
Edit - I failed to mention that I went through the whole brake adjustment process and it was do-able.. I just hated opening the release for up hills...

the new wheels should suit you fine. i have a similar build and the wheels are tough as nails:
rims- dt swiss 1.2 (same as 585 just a different decal)
spokes- 32 3x competition
hubs- white industries rear/ campagnolo record front

i am 175lbs and ride these on a fixed gear road bike (700x23) over cobble stone, rough roads, and up some pretty stout climbs. due to being a single speed most of these climbs are done in an out of saddle sprint. if they flexed badly, i would know.

OP:
let u know what wheels you have and what you weigh. it could be the fork/frame, but my guess is its the wheels. there are plenty of options out there. i wouldnt settle for having to open the brake.

The one pair of Aksiums I've had my tensionmeter on were terribly undertensioned. No wonder the rider using them kept breaking spokes. If you feel like giving those Aksiums away, I'll gladly take those crap wheels off your hands

It is possible for strong riders to flex a frame. You probably notice the frame flexing in other ways.

IF you are flexing the frame bad enough to rub the brakes, you MIGHT be rubbing the tire on the chain stay. On a carbon fiber frame, this is a dangerous situation. The tire rub will cut a groove into the carbon fiber. This will even happen with steel frames. HOWEVER, damaged, cut, or scored carbon fiber is VERY prone to catastrphic failure. Check to be sure. Most often, this will be on the left side chain stay.

If you are flexing your frame, making adjustments like opening up the brakes is a dangerous bandaid. You need a stronger frame.

Thanks all. Here are the answers to some of the questions:

1. I have the stock Shimano wheels that came on my 2007 Scattante: Shimano WH-R561-L, 16H front and 20H rear.

2. I am 6' and weigh 195.

3. I have adjusted the brakes a little looser, but I don't want to go much more. I really don't want to open the releases for downhills.

4. After reading the responses I am certain whether it is the frame or the wheels.

5. If it is the frame, I will examine the chain stay. I will also look at the spoke tension.

its not your bike.i am 6ft 175lbs and ride a scattante xrl frame. it is plenty stiff for sprints and fast climbs.

check the spoke tension on your wheels but my guess is they just dont have what it takes. i would spend $200-$300 and get a set of wheels that have the following:
spokes- 32
hubs- 105 or ultegra
rims-open pro, open sport, cxp33, or cxp22

Let's rule out the simple stuff first before replacing wheels. Make sure that the hubs are adjusted properly. Wiggle the wheel side-to-side while it is on the bike (and you are off it, of course). If there is motion then adjust the hub or have it done.

Check your rear axle clearance. If the QR is clamping partially to the axle, the assembly can shift in the dropouts under load while appearing to be solid when static. Look for rub on the outside of the dropouts, under the QR ends.

While folks are telling you to check the spoke tension of your wheels, you also need to understand that once wheels are tensioned into a working range, increasing the tension does not make a wheel stiffer. Stiffness is determined by the elastic constant of the materials (Young's modulus) and remains the same regardless of tension. The only to get a stiffer (less deflection per unit force) is to use stouter materials, either more or larger gauge spokes, or a heavier rim, or both.

Test for deflection by holding your seatstay and pushing the rim across at the brake shoes with your thumbs. You can also test the lean flex by leaning the bike over a bit and gently pushing frame at the rear dropout with your foot, while watching for flex at the brake shoes.

If, after aligning the wheel as well as possible and checking for hub play, it still flexes enough to touch the shoes while riding, and the brakes are already as open as you feel comfortable with, only a new stiffer wheel will help. Before you spend dough confirm that it'll make enough difference with a borrowed wheel.

One last, but maybe the best, option is to find a rear brake caliper with a lower leverage constant; one which opens/closes more for a given amount of cable pull than yours. That will give you extra shoe travel allowing greater clearance, but still function effectively, though it'll need more squeeze force for given stopping power, which is rarely an issue for rear brakes.

this is good advice and i do believe these hubs have standard bearings. it is very possible its just a simple adjustment. i just have my doubts that 16/20h wheels will make the OP happy.