Not Receiving Standard SMS on iMessage for Mac
Unfortunately, Messages for Mac only sends iMessages, and unlike Google Voice, doesn't send SMS messages. This limits Mac Messages to only be able to send and receive iMessages from other iMessage enabled devices (such as iPhones, iPods, iPads, and Macs). Also, another result of this is the fact that only iMessage threads will sync over to your Mac - SMS threads won't (as you have noticed).

This is indeed a limitation of the software, and not a configuration problem.