I'm going with cold damage on this one. I'm looking at the weather report for your area (Newport, Oregon, right?), and it says the nighttime temps are in the 40's. That REALLY cold for orchids.

I received a shipment of orchids when our temps were in the 40's, and the seller had not included a heat pack like I'd requested. Some of the plants in the box arrived with severe cold damage. The plant that got the worst of it was an Oncidium alliance hybrid. It arrived with massive amounts of blackened tissue all over the outside of the bulbs, and black spots all over the leaves. The leaves are slowly turning yellow, and they are covered in black spots that look pretty much identical to yours.

If that can happen to a plant that's inside a box, wrapped in layers and layers of newspaper, it can certainly happen to one that's sitting outside, exposed to the elements. I think it's probably still too early for you to put your plants out...you'll want to wait until the night time temps don't drop below 55...and that's on the low, low end of temps.

The other thing to consider with cold temps is that any plant that is sitting in very wet conditions experiences the cold more harshly than one that is dry. Miltoniopsis plants like to stay pretty moist and they have very thin leaves, so they already have a higher probability of taking cold damage than some other, hardier orchids.

Here's what the American Orchid Society has to say about Miltoniopsis temps:
"Many people have the impression that miltoniopsis are "cool-growing" orchids, like their cousins the Odontoglossum crispum types. While miltoniopsis certainly will not tolerate the extremes of temperature that a cattleya or vanda might, they by no means require - or like the almost frosty treatment in which most "odonts" delight. Night temperature is not a critical factor in our experience, as we have grown our miltoniopsis with both paphs (55-58F nights) and phalaenopsis (65-68F nights) with good success. Night temperature should be kept at or below the high range, however, for best growth. Miltoniopsis will tolerate down to 50F at night if kept on the dry side (but not bone dry!). Young seedlings will, of course, prefer the warmer range of night temperature while mature plants should be run at 58-62F nights."

So there you go.

As for what to do with the damaged leaves...you'll want to keep an eye on them so that you don't end up with a secondary infection. You may need to trim off any severely damaged tissue, and the full extent of the damage may not show up for the next few days, but once it all settles out, the plant should recover. Put your plants outside when the temps are solidly above 55, if you decide to continue to put them outside at all. Everything I've read says that these guys don't need the temperature drop to flower well anyway. I think your plants will flower when they're ready. If you're sure they have enough light and it's not too hot, they should reward you with some flowers when the newest growths are mature.

Hope that was helpful! Good luck!!