iOS 10, Messages has bifurcated chat history with my wife
This type of behavior is usually caused by Messages between phone numbers and iCloud ID's (typically your iCloud email address). You can click the target user for a message at the top of the thread (macOS) and it will show which address it was exchanged with (phone or email). On iOS, tap the circle with the username or photo at the top of the thread and the "recent" tag will be on the address used for those messages. See if the two threads are different. 

Also make sure your Mac is enabled to send and receive messages from your phone numbers on both Macs. This is not the default for the Mac, though it is for the iOS devices.