Here are some tools that might be helpful with troubleshooting your MIDI files:
WARNING: These programs might interfere with MultitrackStudio.
I installed these on my system and MultitrackStudio started freezing.
Use these programs at your own risk!
* MIDI Disassembler/Assembler
* MIDI File Converter
http://www.borg.com/~jglatt/progs/software.htm
You can use MIDI Disassembler to view the contents of MIDI files as text. It can convert those text files back to MIDI files and has options for filtering out or changing data.
MIDI File Converter can convert MIDI files between Type 0, Type 1, and Type 2 Standard MIDI File formats. Type 0 is a single MIDI track with all MIDI events on it. Type 1 is a multitrack MIDI file. Type 2 is a MIDI pattern file (rare and not the same as MultitrackStudio's pattern files).
Using MIDI Disassembler I noticed that Jazz++ Sequencer add's system exclusive junk to the beginning of MIDI files. It also revealed that the sustain pedal was in use, which is useful since sustain pedal data is not visible in some sequencers.
You can also use MIDI Disassembler to convert Note Off events to Zero Velocity Note On events. This is useful for some older MIDI devices.
OK, THE SAFE STUFF:
The rest of the source website has some very interesting information. In particular, it describes in great detail the contents of MIDI files and transmissions including timecode events:
http://www.borg.com/~jglatt/