Okay, here's a somewhat thought out theory...
Don't mock it until you see how it can explain some things.
It's called the expansion of everything theory. Basically, scientists have known that the universe as a whole is expanding. It's not as though the centre is static and the "outer edges" are getting farther away from it, but rather that the entire fabric of space time is being stretched out like a balloon so that every point in space is moving away from every other point. It was thought that condensed objects like people, planets, solar systems, and even galaxies were held together by gravity and were not flying apart due to this expansion.
Well, maybe EVERYTHING is expanding, people included. I'm saying that perhaps our molecules are expanding, but so is the space between them, all at a rate that is proportional, and so we keep our shape (I can explain further if required for clarity).
Where this comes in to the physical contraction of objects at relativistic speeds is this:
Take a spherical object and let's say it is expanding at a radial velocity of v. In relation to the centre of the object, the point on the surface of the sphere along the positive x-axis is moving at a velocity of +v, and the opposite point on the negative x-axis is moving at a velocity of -v. Now, move this object as a whole along the positive x-axis at velocity u.
Now using the relativistic velocity addition equation, you can see that the difference between the relativistic addition of u + v [rel(u+v)] is less than 2v more than the relativistic difference between u - v [rel(u-v)].
Normally, you have:
u + v - (u - v) = 2v
but using relativistic addition you have
rel(u + v) - rel(u - v) < 2v
Where this leaves us is that because the object is not moving in the y- or z-directions, the difference between the expansion rates of opposing sides in those directions is 2v, while in the x-direction, the expansion is less than 2v, thus, leading to an apparent contraction in that direction.
This is really rough, but it has some potential.