I am having the same issue and its pissing me off I cant find a solution other than render an image sequence.
I have a huge library of AE uncompressed AVI footage that used to import and track fine but does not anymore. I know its best practice to do that anyways but often there is a unexpected or creative need to track something quickly on the fly.
I think this atarted after one of the After effects CC updates I installed a month ago. I NEVER had this problem in the past as well and the additional operations, file and time mangement has caused disharmony in my workflow and addiction to Valium