Your display options in Contacts is probably set to show phone AND SIM contacts (and/or google contacts too)

Open contacts, Menu>More>Display options and check what you have phone, sim and google set to

 

I'm having a similar issue with my HTV EVO 4G. I went through, and deleted/combined in the 'people' section, but when I go to send a text, I'll start typing in someone's name, and several contact numbers come up, even though they're not all listed in the people section.

 

I too had this problem but cured it by doing this
i backed up all my contacts to Google gmail,then
i deleted all my sim contacts by using my wifes old mobile and restored them from Google gmail ,by doing this the contact pictures are there every time
and never any duplicate numbers.

 

If your flashing roms and backing up using Google you've probably created duplicates on your Google account.
To find out/ fix open Gmail from your desktop
> click contacts on the left
> all contacts tab above your contacts

If you have duplicates simply:
> select all
> more button
> find and merge

hope this helps.