It has to do with "who wrote the history."

In many cases, these Pharaohs were first known to western history through the writing of the Greeks. They had a different alphabet system and so when they were confronted withnames in another language, they approximated them -- just as we here in America approximate many First Nation names and words (another example is the modern multiple spellings of Qaddafi's name or the capitol of China, Bejing/Peking/etc.)

The Greek and Roman histories were used to identify pharaohs to make it easier for scholars to match the Egyptian name with the Greek/Roman source. They are generally known by both names to Egyptologists.

-- Byrd
Moderator, Hall of Ma'at