I was having this same issue for one of my contacts. In the stock messaging app, the SMS thread would show his phone number but not his name. However, if I opened up the contact, then used the slider at the bottom to view the SMSs that were associated with him, then the thread showed his name. I did a couple of things to fix the issue, not sure which of them did the trick though. I edited the contact to make sure all of the numbers associated with him were entered in this format: (123) 456-7890. I deleted all existing SMSs from this person and made sure I was not the first to text him so as I was not the one to create a new thread in the stock messaging app. Instead, I made sure that an incoming text message from him was the SMS that created the new thread. I linked and unlinked his Google contact and Facebook contact. Again, not sure which of these fixed the issue but its now resolved. Hope something I listed helps you out.