Ruby 1.8: 178 175 chars
f,n=$*;b=IO.read f
n.to_i.times{s=b.dup
s.size.times{|i|t=([82,1,-80].map{|o|b[i-o,3]||''}*'').count 'X'
s[i]=t==3||b[i]-t==?T??X:?.if s[i]>13};b=s}
File.new('out.txt','w')<
Newlines are significant (although all can be replaced w/ semicolons.)
Edit: fixed the newline issue, and trimmed 3 chars.