I've seen this problem since the very early days, and it seemed to be getting better around 1.2, but in 1.3 betaX I'm seeing perhaps the worst behavior yet.
Vexing things include: 1) parts on legacy designs that are only there visually (no effect on ship stats) and cannot be deleted (e.g. a Singularity Driver). 2) Corruption of the images for components (e.g. Photonic Torpedo). 3) New designs that will not generate an image in the Shipyard list.
Something funny is going on with the image building b/c when #3 happens I have to wait quite a while after clicking OK (accept?) before the Shipyard displays again.
Could this be a result of a humble-but-otherwise-workable video card (NVidia GEForce2 MX 400)?