Command line mod support was a feature added with Version 1.41. Unfortunatly, it donta worka no gooda.
Prior to 1.41 there was no command line mod support.
Actually Mods
can be done on PBW with Version 1.41, or 1.30. (1.35 doesn't work on PBW at all because of a different bug) However, because of the command line mod feature not working, it would require a separte SE4 installation on the server, with a different path.txt file. This is a can of worms because of the extra use of hard drive resources. I think the plan is to wait until the next patch to start taking mods again.
Geoschmo