There are no problems with the 539 BC date.
The problems are with BM 33066, which is riddled with errors. The Watchtower uses two lunar eclipses from this tablet to yield the 7th year of Cambyses II, and then using the economic tablets, count back through the reigns of Cambyses and Cyrus to get 539 BC.
However, I believe most scholars use all the other astronomical tablets that are more reliable, like VAT 4956, and count forward using the economic tablets.