Names Missing In Inbox

As you correctly pointed out the usual explaination for this is duplicate entries. As this is not the case, just out of pure curiosity do you have a backup of these numbers on the sim directory? I'm pretty sure it shouldn't matter but may be worth trying, not tested this myself as i never keep numbers on my sim, always a copy on the mem card. If that doesn't help then i feel you may have a corrupt mail directory.
What i would do is firstly delete all your messages from your inbox, outbox, reports and so on and also delete any email accounts you may have, so it's as close to default as poss, restart your phone and see ho that goes. Then if still no good, you would need to manually delete the entire mail directory in the system itself, which, if you keep your messages on the memory card is only a matter of removing the memory card and putting it in a card reader on a pc then navigate to \private\ and finding out which folder in there contains your messages, it will contain folders like 0,1,2,3,4,5,6 and so on. If you find it remove the whole directory. If you keep your messages on the phone memory your a bit stuffed, unless you've hacked your phone and can disable caps in order to gain access to your system folders, if so then follow the same procedure as for the mem card.
Lastly, another thing i would do is do a backup of your contacts to the memory card, by marking all, then options, copy, to memory card. Then you will have a folder on the mem card in e:\others\ called "contacts" then manually go through al the contacts in an independant viewer for .vcf files and make sure you have no duplicates anywhere, then delete all your contacts in the phone, then copy them back from the memory card using, options, copy from mem card in the contacts app.
Hope any of this helps, i've not had this problem, but thats the route i would go down if it did happen to me.

i decided to delete a few messages from my inbox and it solved the problem. not sure why though.