So I did finally fix my problem. Thank you for the responses, none of them directly solved my problem but they did prompt further examination of my code. After some trial and error I finally got it working. I had originally moved the platform_device structures for each usart from /mach-at91/xxx_devices.c to my loadable module. Well for some reason the structures weren't getting the correct data to map to the hardware, I suppose because it wasn't correctly linking the symbols from the kernel (never got an error message though) and so some of the registration functions weren't even getting called. I ended up moving the structures and platform_device_register calls back into the devices file. I also decided to keep the driver for the console built-in using the original atmel_serial.c driver. I had to change the platform_device name for the console in both the devices file and in the built-in atmel_serial.c file in order for it to not conflict with my usart ports driver. I found that changing the platform_device and platform_driver name for the usarts from anything but "atmel_usart" resulted in usart transmission failing. I really don't understand why, but i'm just leaving it as atmel_usart so it works.
Thanks again to everybody who responded to my problem.