If the flasks are sealed you wouldn't think the environment would make much of a difference to whether they go mouldy or not... i feel for ya though, the last flask of phals i bought also was contaminated in the flask. I took them out, fungacided them, and still have lost about 1/4 so far to rot. In comparison my other Phal flasks have had 100% success so far.
if i can suggest though when you do deflask them that if you put them in an aquarium, put a small fan in there on a timer to keep the air flow up. A closed warm humid space will lead to mould in a lot of the seedlings.
This is my setup that i find works well:
Vermiculite in the bottom soaks up the water, keeps humidity up, light provides heat, fan provides air movement, fan on 15 mins every hour, light on 10 hours a day.