This discussion and my experience say that humidity levels can cause serious changes. I'm dealing with this problem now, for the first time ever after having canvassed many canoes. This one is canvassed, filled and painted (painted months after filling). When humidity levels increase, the canoe looks fantastic. When humidity goes down, wrinkles appear. I've let it go now for several months and the problem persists - I see changes every time a front passes through.
But here's the twist - this only happens on one end of the canoe, and that's important. I started with a filler from a gallon can that I had opened and used half of a couple of years ago. The filler smelled awful, and the oil had turned nearly black. Still, I tried it after adding a little bit of liquid mold killer ("MX-3 Complete Mildewcide", 3-iodo-2-propynyl-butylcarbamate). The mildewcide says that it is appropriate for water-based and oil-based paints (which makes no sense to me), and it didn't seem to mix well with the filler. The filler went on poorly in that area and only dried after a MUCH longer time than usual. When I realized the problems there I switched to another batch of filler for the rest of the canoe. It's only on the area of the first filler batch that the wrinkling occurs.
I'm not sure what all of this means or how it relates to others' experiences, but hopefully adding this information will help us all better understand what's going on when we have these problems.