My plugin works fine with release 0.3.1. I just tested it. I downloaded a fresh 0.3.1, then installed my 1.3.2 plugin. Works fine. Release 0.3.1 uses jquery 1.3.2. This is packaged with roundcube, in programs/js/jquery-1.3.min.js.
I also tested my 1.4.0 version on 0.3.1, works fine as well. I see no problems as you're describing. That doesnt mean there arent problems, just that I dont see them. Do you get any errors in your error log?
Why are you trying to install jquery 1.4.2 on roundcube 0.3.1? That probably does not work at all, as roundcube may use features that are deprecated or not working in jquery 1.4.x. With roundcube 0.3.1, you do not need jquery 1.4, and should be able to use my 1.4.0 version without problems.