Well I did have it under vacuum for 12 hours before infusing in an attempt to boil off moisture. Got careless after that. 

After reading everything in this thread I'd even recommend drying the flax in an oven before infusing it. Might be overkill, but unless it is stored under dry conditions it might absorb a considerable amount of water. I have some cotton flox in a small glass jar, someone left it open for an unknown duration and it started to become clumpy. The flox in the original plastic bucket it came in is still dry after several years.

Hmmm, thanks Warren. I'll try baking it. It definitely seems more like a residue on top of the resin though, it's almost like greasy finger-prints that just won't come off. 

Flax is very hydroscopic so wicking could be an issue. The surface of the resin would be hard but wicking might be enough to take moisture deep in.

I'd try baking it off and see if it drives out the moisture as it postcures.

Warren Penalver
Easy Composites / Carbon Mods - Technical Support Assistant

Hmm it's possible as this is the first time I have used an infusion specific resin... However I washed both trays when I removed them from the mould, and that didn't cause any issues? It was only after trimming that the problems started... 

i have found that particularly IN resin will take a long time to cure and will absorb water and become cloudy if worked before it is fully cured. My experience involved wet sanding a  part that had been made with IN resin and fished with coating resin. When i wet sanded the coating resin everything was fine unless i sanded through to the IN resin underneath and then bad things started to happen in much the same way as you are describing. Cloudyness - patches moving around, spreading and no hope of improvement. the more you work it the worse it gets. I would try either baking before you do any finishing. Or . dry sanding then vacum and lacquer with 2k all wearing gloves to prevent any contamination on the surface. I do something like the later but i finish with coating resin not 2k as i need a very durable finish. Basically its the water in my opinion. 

weird stuff! can not find any possible cause and never read or seen about it before...

Amine blush is caused by water vapour and CO2, so it is unlikely to appear in an infusion. It's also weird that it appeared days after it had cured, amine blush should appear during curing, so I assume it's something else.

Yes I had considered that, but given this residue is on the surface of the epoxy and not underneath, I considered it unlikely. 

Probably not an explanation for your problem, but have you considered water wicking into the fibers on the exposed ends?