Hm, no that should not make a difference, all vl stuff recognize table prefixes.
Did you uninstalled the old before uploading the new? ( clicking the delete button )
Are the new fields in admin -> settings ->twitter ?
to use 1 twitter application you need to allow your other domains to join in the fun. Login to your dev.twitter.com account and click on @Anywhere domains tab, then enter your other domains and you should be all set.