I have an annoying problem that frequently occurs on both, my laptop and PC - both of them are equipped with adequate 8 GB RAM, i7 CPU and NVidia 630M & GeForce GXT 770 GPUs, Windows 7 Home (64) and same software. I normally edit my video media with Vegas Pro 12 as a project (see settings attached), render the image as m2ts and audio as ac3.pro and produce final Blu-ray with DVD Arch Pro 6.
Upon importing MTS video files from my Sony HDR-TD20VE 3D cam into Vegas Pro 12 and overlapping the media on the timeline with, perhaps, transition features (eg. clock wipe, 3d fly in/out ...etc.), I often notice popping, or clicking noise when previewing the timeline. These noises are transferred into the final product (video m2ts audio ac3pro) when rendering. The media is absolutely clean. The popping noise does occur only at the transitions (where two media files overlap). This does not happen at every transition. When I separate the two media files on the timeline, the pops do disappear, putting them back again, makes them come back again.