Hi Wesley,
as some responders already indicated, midi-files come in all "tastes and flavours", i.e. may vary considerably when looking into the files data.
I suggest to download Sekaiju (
http://openmidiproject.osdn.jp/index_en.html ; see the link on the page to set it to English) and investigate a few midi-files.
E.g. you'll see files with and without heavy use of synthesizer specific messages, as well as various assignments of instruments and channels. After checking a few files you should have an idea, what might be the cause - and what to do about it, e.g. with Sekaiju.
Best, Michael