I too have this issue...
I purchased the RT-AC66U H/W Ver. A2 on 11-3-2012 and have been happy with the product for the most part. I have been experiencing an issue with the 5Ghz band, starting with the original Firmware 3.0.0.4.140 all the way through to the current version 3.0.0.4.266. The issue is that the 5Ghz band drops its power down by 20 to 25 dBm after being on the air for anywhere from 2 hours to 3 days. I use inSSIDer to monitor the routers power out in dBm from a fixed location. I have played with the “Tx Power adjustment” and have found that 90mW is the sweat spot, anything above or below this does not give me an increase in range or dBm. From my laptops location, approximately 5meters from the router through 2 walls, I get a -45dBm signal when set to 90mW. This gives me excellent coverage and data rates throughout my house. When I notice the signal level drop on my other devices (anywhere from 2 hours to 3 days) I go and check inSSIDer on my laptop and find that the signal level is down to -70 to -75dBm. I log into the routers “Professional 5Ghz” page and hit “APPLY” without making any other changes and boom the signal jumps back up to -45dBm.
I do not have any issues in the 2.4Ghz band, it is rock solid all of the time.
Current settings:
2.4Ghz mode: Auto, bandwidth: 40MHz, Control Chan: 11u, WPA2/AES, Tx Power 90 mW.
5Ghz mode: Auto, bandwidth: 80MHz, Control Chan: 44, WPA2/AES, Tx Power 90 mW.
Another thing I noticed when using “Asuswrt-Merlin - build 3.0.0.4.264.22 (15-Dec-2012)”, is that I saw no change in temperatures for either radio.