Sorry about the issue with the pads, aside from the two things I mentioned I haven't heard of anyone ever having trouble with this. I've never heard of any MKIII having different components from the others; It is a possibility.
The caliper must move smoothly along the glide. If it doesn't the brake pads may wear unevenly and the caliper can twist introducing a shudder.... and probably some other stuff I haven't personally experienced.
Pull the caliper off the glide and using a good cleaner (I believe I used brake cleaner but it may have been carb cleaner) and a thin metal bottle brush clean the inside out very thoroughly. Then clean the glide (glide, guide, track, rail, I've heard it called a dozen things.); inspect for pitting. Replace it if it is heavily pitted. Once its all clean, lube both sides thoroughly and reassemble test the fit to make sure it moves freely. Make sure you use a lube specified for the task!
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