Todd, check closely for the rip/tear. I hope it's from the wind as well but this has happened to me twice that a dog has torn a liner. The older the liner is the more easily it can get ripped. Like started above both times I let the water level drop until it stopped and started looking, each time it was still below the water line by about a 1.5"-2" below where the water stopped falling. I was losing water in my pond as well and thought it was evaporation. Went in the pond to do some maintance and while moving things around and pulling a few Cull koi one of my rocks on the side started sliding down. when I lifted it to put it back in place I found where my water was going. During the tropical storm this year water got behind the liner and floated it up in places. I guess this caused the liner to slide away from the edge and the edge of the liner had slipped below water level. a little tugging and back fill and I got it set back in place and lord and behold, I went from turning the auto fill on all the time to once a week for about an hour and a half a week. Just got this month's water bill in and my water usage went down by 8,000-10,000 gallons! Now I'm sure some of that was due to not having to water potted plants as much but a good bit was the water going in the pond. I was surprised at how I could notice on the water bill though the increase in usage from the time of the storm to the time I got the liner reinstalled correctly. VERY noticable on the usage chart of the water bill! Not so much on the cost. Cost wise in only changed the water bill by about, $8
A little tip I found works pretty good when looking for a leak, If you know of a suspected area, instead of feeling for a tear or split, push the liner toward the dirt banking, If there is a leak, water will retain behind the liner. Pushing the liner in will cause the muddy water behind the liner to move in and out through the split causing a small amount of muddy water to appear. if you go along the edges and do this before actually stirring up the pond a good bit of the time it will show up and show you where the tear is. the key to getting this to work is balancing the water both behind the liner as well as in the pond. (letting the pond drop until it stabalizes) If the tear is a inch or two above or below the water line it's a lot easier to spot the muddy water coming into the main body of water, if the tear is a good bit deeper the water pressure in the pond actually causes a seal near the tear and makes it harder to spot.
Good luck, Again, I hope it's evaporation! not a tear!
Good luck figuring out your problem. I hope it's the wind, you can always put something up temporary to shield it so it doesn't blow off the waterfall. 
