I don´t know the Atlona in particular, but usually, these kind of devices have a "passthrough" setting to (well) just pass through the EDID information it gets from the display down to the connected source/AVR.
EDIT: Just had a quick look at the manual: via the webfrontend of the matrix, you can assign specific EDIDs to each input. I´m assuming there´s something wrong with the settings, perhaps based on your previous setup.
EDIT: Just had a quick look at the manual: via the webfrontend of the matrix, you can assign specific EDIDs to each input. I´m assuming there´s something wrong with the settings, perhaps based on your previous setup.