The key at 4-1-4-1 is the DMC, who gives the center more stability. That is where 4-1-2-1-2 focuses the attack (if played in a normal way). And with the offensive motivated wingers (as July described), you can play nice counter attacks. I made very good experiences with it against 4-1-2-1-2, too.
But if it is a counter formation, I don't know. There is more the match engine considers. Sometimes I noticed special ability players can turn the outcome of a match completely besides the famous random effects. :s
I had problems with 4-5-1V as well against 4-4-2 in the CL some days ago (won luckily by standards), but I believe it was no normal 4-4-2, but a motivated one.