They dont. When they encountered the newly regenerated Christopher Eccleston, David Tennant, Matt Smith and even in the old series with Patrick Troughton ( the 9th, 10th, 11th and 2nd Doctor) The Daleks did not know he was the Doctor until he stated so. They do however recognise he is a threat and this is what leads to them recognising the Time Lord.
Sometimes they do recognize him after regeneration. But probably this is just because (at least until the Last Great Time War) they have time-space visualizers (as in "The Chase") and keep records of where, when, and with which face they've spotted their greatest enemy.