The initial release of EP3C datasheet stated that MSEL must be hardwired to GND or VCCIO; later VCCIO was corrected with VCCA. Probably your boards were designed using the preliminary datasheet as a reference.
Anyway, MSEL pins are powered from VCCINT but there is no specification about maximum voltage allowed. I don't believe the difference between VCCA and VCCIO itself matters. The problem could rather be the fact your supply rails set up at slight different times and you device gets the wrong MSEL configuration.
In your situation I'd follow the simple basic rule: don't change anything if it works. :-)