a converter is not covered under 5/100 unless you bought an extened warranty. there is a 5/100 powerstroke warranty that covers just the engine.
next odds are its not a converter. the 5r110 is not know to have that issue or really any other issues. its a great unit.
the 06/07 trucks seem to have a bit of turbo lag and there may be an incress of lag felt if the pcm was reflashed to vxcf9