I rendered a project whichj had some BBC Optical stabiliser, BCC noise reduction, BCC magic sharp on a few various random clips throughout.
After rendering to blu-ray into Architect Pro 6 IU them watched the footage back only to find that wherever a BCC plugin was used there was some really weird behaviour like letterbox lines wobbling up and down on the stabilised clips; strange reduced aspect ration on one clip with noise reduction; some picture in picture oddity where a clip had overlapped another in the project??
None of these strange things were in the project until it was rendered out. When removing the plugin it was ok.
I also found that rendering to Sony AVC for architect 10mpbs instead of 16mpbs helped.
I don't have these plug-ins, but I can visualize how some of this behavior might be logical based on how the plug-in operates. For example, a stabilizer may be dynamically adjusting the degree of cropping applied to video to achieve a stable image. I can see how that might cause the size of a letterbox to be adjusted in the same dynamic way which would explain what you are seeing.