Hey,i've mostly seen that this problem is only there in those N900 phones which come with pre-installed MSCIM.My solution is simple and it doesnt have any side-effects,so give it a try.I'll go through it step-wise..
1: Open application manager and go to uninstall
2: Uninstall MSCIM or SCIM that you have
3: Open X-Terminal
4: sudo gainroot
5: cd /etc/event.d(There's a space after 'cd')
6: ls
7: After 'ls',see if 'scim' is there in that list that comes up,if its there just remove it with the following command.I'll just write it as '8'
8: rm scim
Now type '9' and '10' exactly as i do,
9: /usr/bin/gtk-query-immodules-2.0
10: /etc/gtk-2.0/gtk.immodules
Even if '10' doesnt work,taking care of step '1' to '9' should make the virtual keyboard work.Let me know how it went..