Before you upgrade from dd-wrt to tomato you have changed the firmware file extension from "TRX" to "BIN"? If not, here you're wrong.
Try this now:
1. Download "ASUS-RT-N16-RECOVERY.EXE" from this location: http://www.4shared.com/dir/v1BuINP3/Toastman_Builds.html#dir=79333541
2. Download latest Asus firmware from Asus support site: http://support.asus.com/Download.aspx?SLanguage=en&m=RT-N16&p=11&s=2
3. Connect your computer's using network cable to one of the LAN ports of the Asus router. DISCONNECT any others cable from router (lan or usb).
Manually set your computer IP address (in the TCP/IP properties of the LAN connection) to 192.168.1.2, network mask 255.255.255.0
4. Plug in the router while holding the reset button on the back of the router. Keep the reset button pressed until Power LED starts blinking slowly. This puts the router in recovery mode, which is necessary to flash using the Asus Firmware Restoration utility. If you try using the restoration utility and the router is not in recovery mode or is not connected it will say, "No wireless device in recovery mode is found".
5. Run "ASUS-RT-N16-RECOVERY.EXE" which you downloaded in step 1. In "ASUS-RT-N16-RECOVERY.EXE" browse for the firmware image you downloaded in step 2 and click Upload.
……if everything went fine go to step 6
6. Do a hardware reset and after that reinstall DD-WRT firmware. After that again CLEAR NVRAM.
7. Change extension of Tomato firmware file from "TRX" to "BIN".
8. From DD-WRT web-gui browse for Tomato file with extension "BIN" and now upgrade. For sure, wait for 10 minutes.
READ TWICE AND APPLY ONCE, because if you does that, everything went fine. On DD-WRT pages is an tutorial that explain that.
NOTE: - points 3, 4 and 5 is a COPY / PASTE (and adapted to this situation) from Lassik's tutorial "Installing on Asus Routers (RT-N16 and others)". Thanks Lassik.