Please perform the following to find differences between two similar PCB's:
1. Create a New Job (Menu: File / New / Job...) and name it after your first design (or part number).
2. Import all data from that job.
Note: If Gerber/Drill, try using AutoLoad (menu: File / Import / AutoLoad...). IF ODB++ than use ODB++ Import (menu: File / Import / ODB++)
Once you have loaded your first design, now lets create a second job and import that design.
3. Create a New Job (Menu: File / New / Job...) and name it after your second design (or part number).
4. Import all data from that job.
Compare Jobs: Go to menu: Tools / Compare Jobs and Layers / Compare Jobs...
The easiest is to perform Graphical Comparison -- View each layer and if "Yellow" means the design is the same. If Red/Green then there are differences.
Note: Then you simply turn on/off any layer that you wish to compare.
Here's a sample tutorial demonstrating how to compare between gerber Layers: