I was searching for MIDI tools over the weekend and ran into this page which has a very similar first sentence to what the OP (originally) was. Left me wondering how these offending MIDI files were created.
 
I believe you can send a PM after 25 posts (?) so if the OP posts a few quick comments, you can PM swamptooth (or simply post a link to one of those files in a reply with the hyperlink split apart (e.g., DOT com, etc)). Having one of these offending files to examine would help the MIDI heavies here help you.

There are a variety of "midi monitors" that simply read a stream of data and print each event to your screen in "english-ish".    The very old midi site, "midi-ox.com" is still safe, I believe (you never know what 'free downloads' may bring you ... )