Hi Martin,
I suspect that what you're hearing may be due to a MIDI cc in the file, not the synth itself.
If using Composer, you can take a look at what MIDI controllers are used in a file. Using Graph Over Notes, click on the "Ctl?" button, and look through the list of controllers. Any that are in the file will be marked with an asterisk "*". Some culprits that can make things sound weird are Mod Wheel, Expression, Effects, "Sound" related ones, among others.
To see if the controller in question is causing the issue, select it in that dialog, and then delete it's graph (select the staff/staves, then hit "Delete" on your keyboard). If the weirdness goes away, that was it
If it doesn't, try another controller graph.
If you use "found" MIDI files, sometimes they are sequenced with a particular synthesizer or sound library in mind that uses these controllers. While the file may sound spectacular with that particular synthesizer/library, it can sound odd on others.
Let us know how it goes, or post a copy of a file that you're having the problem with and we'll take a look at it.
ttfn,
Sherry