If protected mode refers to encryption (WEP/WPA) then leave it on; the performance hit is negligible.
With the firmware, .bin is a pretty common extension for a firmware file. Normally there is a page in the router administration where you can upload the file to the router, and it will automatically upgrade and reboot itself when done.
Have you tried updating the driver for your wireless adapter as Dale suggested? I have a feeling this might solve the problem.
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