It is very likely that you are putting too much stress on the frame when you are cycling due to your power stroke.
It took me a long time to train myself to avoid standing and powering the bike through the acceleration of starts, or even powering through it while sitting. I've long since learned that while I have plenty of power, I actually am able to transmit it more effectively to the wheel using a faster cadence with lower power.
Try to start out in lower gears so that it's easy to get up to 90rpm quickly (quickly, as in within dozens of feet, while you are still accelerating). If you don't know your cadence, or have an easy way to measure it, the disco tune "Stayin' alive" is just over 100bpm. There's a lot of other music you may be familiar with that is about 90bpm, you can do a google search for "90bpm song" and you'll find lists such as this: http://www.edenathletics.com/90bpm
The location of the stress fractures really suggests that you are standing up to push more power into the pedals. If you are doing that, stop standing - road bicycle frames are not meant to take the pounding that this type of riding entails. The standing position puts a tremendous amount of force on that particular joint, and the pedals are not long enough to really transfer that energy into the chain - you are wasting a lot of power flexing the frame. It you are a fan of geometry and physics, imagine putting the frame on two stands where the wheel hubs are usually located. Now place a bouncing 1/2 ton load on the bottom bracket. You'll find the stress fractures are disturbingly similar to the ones you are experiencing - the two triangle shape of the frame will force the top tube and seat up, while the bottom bracket is forced down, leading to fractures in the seat tube. If the seat tube is strong, you may instead fracture the chain stay on the chain side.
If you prefer that riding style, however, then you'll have to settle for mountain biking frames, which are designed for powerful stroking techniques. This is one of the reasons messengers often use mountain bikes - they are standing up a good portion of the time with very powerful strokes to accelerate in very short bursts.
While spinning doesn't allow such high acceleration it is much more efficient in transferring energy from you to the forward motion of the bike. And you can still stand up and accelerate if a situation calls for it, but doing it often is going to fracture your frame.