@lynno I don't feel like this is food related. It just seems more like a behavior issue that is probably related to something you think is "no big deal", but which your dog thinks is "really scary".
So, just a thought -- what about weather? Storms, not your typical rain.... You didn't indicate how long this has been going on, and, I don't know where you live, "but"... the east coast has just had a big storm pass through. I'm asking because I noticed that my 'doodle' didn't want to go for her normal walk the day before Hurricane Isaias passed through. Dogs sense things differently than we do. We might think high winds are just extra windy, but your dog would be able to hear lots of things we wouldn't be able to hear. Like limbs cracking, or falling, pine cones hitting the siding, etc., etc. Noises we can associate with reasons. Noises that your dog might not understand.
So, I'm wondering if you might be in an area that has had recent storms? And do the late night "accidents" occured before, during, or after any of those storms?