I haven't really looked into this aspect very much, but it seems to me that the different
formats and readers involved somehow interact with the file naming and/or the use made
of "metadata". To the extent that the file naming has an impact a "renaming" program
like Oscar's Renamer
http://www.mediachance.com/free/renamer.htm can make changes to the file
names and their structure over all the files in a folder. It has a macro feature as well to
let you automate repeating steps. I use it most often to remove and/or change problem
characters from file nemes. It has sequential numbering functions, also.
Luck;
Ken