I had the same issue before with a beta(pre 6.6), but upon the release it was gone....so, I had no worries...
I wonder if this is something we could figure out without having to bug jcl and wladimir(sorry if I misspelled his name).

I'll go over some things in my scripts..

1) I'm not using a single piece of template code.

2) I've commented all my d3d and engine variables...like tree_range, video depth, trilinear filtering etc...d3d_autotransparency is the only one still set.

3) I'm using shaders with my models(like improved overlay from the wiki)..but this is affecting models that also have no shader applied.

4) there are one or two models that are not affected by this, I've gone over the differences between the models repeatedly to find a "difference" in them...no luck.

5) 9/10 of the time...if a model is unaffected by this, I can copy it (ctrl+d) in wed and the new model will be fine...this is not every time though..??

6) I'm using wdl not lite-c.

Is anything here familiar to you guys?...just looking for similarities, so we may figure this out.