Thank you Jim. I am sure that, from experience, checking the DirectShow setup it's the best way to start.
However in this case I have my doubts. I was mainly asking if anybody else have ran different scenarios, noticed the same symptoms, and if yes, in what configurations. My impression was that there are others - hope there are a few people that don't run MC just for their massive audio collection, but also for their massive video collection. If it's just my problem, I will track it down to the cause and kill it sooner or later. If it's something else...
Following your advice, I did give it a try to CCCP (although I hate codec packs, even if, I admit, CCCP is the most useful). I have uninstalled every filter, PowerDVD, Haali, ffdshow, and install whatever comes with CCCP, let it to register its things, the works. Meaning for MPEG-2 now it uses the MPEG-2 demultiplexer from Microsoft and Gabest MPEG-2 filter for decoding. Filterchains get build up fine (Graphedit) everything (other players) work.
The problem in MC 13 persists. MPEG-2 files get imported as data, tens after tens.
Keeping the same system setup I went back and made a separate install of MC 12.0.534 and thrown at it the most problematic set of files (>1800 video clip files, from various sources, SD, HD, etc). Everything got imported fine, no files imported as data. Anything else I should test?