That's not a lot of information to go by to be very helpful to you.
I would suggest at this point that you perform a "factory default" reset on both of your AirPort base stations, and when completed, use the AirPort Utililty to reconfigure they as required to satisfy your networking goals for them.
I would futher recommend that you place both base stations in the same room during the setup phase, and then, move them to the desired locations once you verified that they are working the way you intended for them to.
A persistent, flashing amber light indicates that any of the several potential conditions may require your attention:
- The base station has not yet been configured because it is new, or the reset switch has been set.
- You have selected a security configuration that is not recommended.
- One of several other conditions, such as a disconnected Ethernet cable or invalid IP address has been detected.
If you run the AirPort Utility, it will show an amber circle on the summary page next to the area(s) causing the problem. Click on this amber circle and it should provide an explanation. Please post back your results.
Are use using the Express to extend or join the Extreme's Wi-Fi network? What is the exact models for each?