I haven't been able to reproduce the "no attachment" problem. What kinds of files are they? Which version of Roundcube are you using?
Roundcube uses the Iloha MIME Library, so maybe you could try installing the latest Iloha Webmail and see if it has the same issue?
http://ilohamail.org/main.php?page=Downloads
Rich
Might be a good test -- the files vary, I'm seeing mostly the typical MS office files, which I can understand them being funny.