Since you don't state your ROM version and so on, I think you might be better of upgrading the rom of your device.
I've not read about any problems on that. As soon as the phone picks the Number who is calling, it associates that to the contact and it's photo ID and name. That is then logged onto the call history.
Be sure you look at the correct place, Call history has multiple entries for incoming, outgoing and missed calls, and an option to see them all, maybe you are looking at the wrong list?