have you tried loading the hex file into mplab and programing chip from mplab ?
verify write from mplab - read of chip

and

and manually blank chip and verify blankness from mplab - read of chip

mplab can be a real pig when it decides your chip can't be used with your programmer
just try an pgm a pic12f1822 with a pickit2 using mplab (any version) it just refuses yet the pickit2 gui has no issues at all . it could send a man to atmel