CR
Yeah, we got some of that rust problem here, too. Anywhere withing a short drive of the ocean, and anywhere where the humidity stays over 80% for a good part of the year!
Your variation sounds a but large, what powder were you using? The larger the grain the more the expected variation, but that sounds way to high. I may not be the best one to ask, I haven't had mine a year yet, and only load a couple times a year, unfortunately. Got a family, a house, honey-do jobs (5 unit bookshelf the current one), and the range an hour away on the freeway. It all conspires to make shooting time somewhat rare.
As to your molds, spray them with WD-40 or another light oil. The first bullet or two will burn it all off, and those get remelted anyway. Use the Rapine mold prep, or make your own with a suspension of graphite in alcohol. Some of the older casters suggest that a mold has to be "rusted in", that your light coating of rust is somehow good. I'm not sure I ever followed or understood that one.