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What is the difference between MSS and MTU? Which one should I be concerned with?

TweakMASTER Knowledge Base article KB0041

MTU is the Maximum Transmission Unit or actual packet size. TCP Receive Window needs to be set as a multiple of MSS which is normally MTU-40 bytes. Those 40 bytes are typical header information attached to each packet, and MSS allows for that packet information.

Sometimes certain connections will use greater or smaller header information. If your connection uses something other than 40 bytes then you may wish to experiment by adjusting your TCP Receive Window size manually with TweakMASTER to an exact mutliple of MSS.

Speedguide's TCP/IP analyzer reports MTU and MSS. It does so correctly for most connections, but we cannot be certain it does so in every case. But it will not hurt to try. Set your TCP Receive Window manually to an exact multiple of your MSS as reported by their Analyzer with MTU set to 1500, reboot and compare your data transfer rates as compared to a simple configuration with MSS = MTU-40 as calculated automatically by TweakMASTER.