Why does `pratchet()` in `phangorn` not find the most parsimonious trees?
Perhaps the tree which you have calculated is not being caught in the search heuristic? Have you tried (as a trial) setting the tree which you calculated as the starting topology, just to check that it is indeed being calculated on by pratchet()?

Alternatively, you could try playing around with the search heuristic settings, like varying from ratchet to NNI, or you could also try using an external program, like PAUP*.