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Ruby 1.9, 77 48 46 chars

r=->w{w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

If empty words are allowed then 56 chars

r=->w{w.empty?||w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

Ruby 1.9, 77 48 46 44 chars

r=->w{w[h=1..-2]=[*w[h].chars].shuffle*"";w}

Disclaimer: I tuned this based on the highest ranked answer - noticed the exact same answer later on. You can check the history that I have kept true to my original idea but changed from ruby 1.8 to ruby 1.9 for short lambdas and shuffle.

If empty words are allowed then 56 54 chars

r=->w{w.empty?||w[h=1..-2]=[*w[h].chars].shuffle*"";w}

Ruby 1.9, 77 48 46 chars

r=->w{w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

If empty words are allowed then 49 chars

r=->w{w||w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

Ruby 1.9, 77 48 46 chars

r=->w{w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

If empty words are allowed then 56 chars

r=->w{w.empty?||w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

Ruby, 77 48 46 chars

r=->w{w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

Ruby 1.9, 77 48 46 chars

r=->w{w[1..-2]=[*w[1..-2].chars].shuffle*"";w}

If empty words are allowed then 49 chars

r=->w{w||w[1..-2]=[*w[1..-2].chars].shuffle*"";w}