http://steamcommunity.com/sharedfiles/filedetails/?id=10785
This changes an existing script, magicSoulTrapFXScript.
You'll notice most of the comments there are "this doesn't bloody work". It has always worked fine for me when I tested it, and no one has posted any problems for the file on the Nexus, so I just wrote it off to Steam users loading too many conflicting mods and didn't worry too much. But then the comments started to pile up and I figured there has to be something going on.
So I checked out the *.bsa in BSAopt and it turns out the CK only packaged the source to the script I changed, not the compiled *.pex file! So the mod is completely broken on Steam. Frankly I'm surprised I didn't get more negative comments than I did. It worked fine for my other mod, Perk Books, which only adds new scripts rather than changing an existing one.
So I guess if you change an existing script there is no way to package it up for SW? A workaround I guess is to have users compile it for themselves, but that's a pretty stupid thing to have to make people do. Someone tell me I'm doing it wrong, or at least that this is a known issue and will be fixed soon. In the meantime I need to take this mod off SW.

Thanks!