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[RT-AC66R] Very Strange Firmware Updating Behavior

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I have two RT-AC66R routers configured as router/AP. They were both running v1.28. Since I was running such an old version, I decided to try out the newer firmwares available (Shibby v1.40, Merlin v380.67_0, and stock ASUS v380.7743).

I took the AP down and flashed to Merlin and then stock checking out both. When I went to flash from stock to v1.40 within the GUI, I get this message...

Invalid Firmware Upload
To comply with regulatory amendments, we have modified our certification rule to ensure better firmware quality. This version is not compatible with all previously released ASUS firmware and uncertified third party firmware. Please check our official websites for the certified firmware.

I read after-the-fact about the non-rollback feature that had been added. I dug out my notes and also saw that I should be flashing from the ASUS Firmware Restoration utility. Here is where it gets weird...

No matter what what version of Shibby firmware I try to flash, after the router reboots, it's running v1.28 again!

I've tried everything...30/30/30, clearing NVRAM, factory defaults, flashing via the built-in web UI, flashing via TFTP, etc. I've tried to flash from stock to v1.30, v1.32, and v1.40. All with the same results. It makes no sense how I can flash from a stock firmware to a v1.40 .trx file and somehow end up with v1.28. I'm at a loss.

My goal at this point is to run Shibby v1.40. Any assistance is appreciated.
Use the Firmware Recovery tool. Tomato doesn't use the newer file header, so any Asuswrt build from the past 12-18 months will refuse Tomato/DD-WRT.

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