If a video upload fails, SmugMug allows you to view your Upload Log in your Settings page to see the error. However, the wrong video resolution causes it to return an "invalid video codec." After trying all different types of formats (WebM, H.264, FLV), I finally succeeded by converting the video from its original format of 400x224 to 320x240, which seemed to resolve the problem.
avconv -i <MP4 input file> -s 320x240 <output file>
There isn't much documentation on SmugMug's site to give you any indication that it's the resolution size that has to be adjusted:
Side note: if you want to flip the audo/video streams, here's how you do it. The first "0:1:0" map parameter means to take file input 0 (since you can have multiple input files) and take stream 1 and map it to stream 0. You do the same for stream 1 of input file 0 and map to stream 0.
avconv -i <input file 0> -vcodec copy -acodec copy -map 0:1:0 -map 0:0:1 <output file>