Kaz, I sent you those models again along with some other stuff... but it
appears I found the problem. At least it solves the problems on 3 different models I tested the "fix" on in which the shields had NOT worked when using PCS to generate the POFs.
Something Bobboau posted about his shield problems was the missing piece.
As I had told you before, the shields only worked
on the back portion of the various models I tried PCS on,
in the area of the thrusters, no where else. I got to thinking, what is so special about that area of the models? I went back and looked at the POF files again with PofDView and remembered what Bobboau said about diddling with the Bounding Box. I got to looking at the bounding box in the HDR chunk versus the model itself and the shields. I noticed that the bounding box was larger than the model by a fair degree in the direction of the thrusters (-z), while it was the same as the model size in all other directions (which puts it
inside the shield's confines. It turns out your bounding box calcuation includes the thrusters themselves but not the shield. On all of my test models the thrusters extend a fair way
past the confines of the shields.
So, I went and pulled up the test models with a hex editor and changed the values of the bounding box in the HDR chunk so that they
encompassed the shield as well as the model (plus a 1 meter margin) and changed the radius to match the new bounding box value. Voila, the shields work now!

So, it appears that the bounding box and radius values in the HDR chunk should be for the entire object,
including the shields. (whether or not the thrusters should be included is another matter, can't think of any reason why they should be included, but it probably doesn't hurt to) In going back and looking at the difference between the Cob2FS2 generated files and the PCS generated files, there is indeed a significant difference in the bounding box values and the max radius values (you can see this in the files I sent you).
Side note, you were right, the shield problem wasn't due to the BSP structure
Note: this has nothing to do with the crashing problem Bobboau spoke of, as I haven't run across that problem. This deals only with the shields properly working.