Common MIDI only allows note on (like C-5), note off and instrument select. Additionally, there's only one channel for drums (channel 10) and there's only 15 instrumental channels.
Try to use the MIDI library when you design MIDI songs. Do not use trance pulse or such, stick to tempo 125 to avoid mistiming.
When you finally do the conversion, be sure that you have allocated each instrument to a unique channel. If you use chords, make a new IT instrument and put the same MIDI instrument in it so you can allocate multiple channels to the same instrument.
Modplug can convert volume set 0 to note off as well as note cut.
If you use MIDI drums, mind that Modplug Tracker has a minor bug. Select the drum chooise above the one you desire to use and you will get around it.
MIDI has no panning, either. Unless you use a custom professional tool.
Since you wanted to know if there's another program you could use for MIDI convertion, I am afraid there's not way too many out there, but try to perform a websearch (google) for "mod to MIDI" or something like that. However, you could let ModPlug Tracker convert your ITs to MIDI first and then fix them up in a program like SynthFont (google for it).