Did you figure it out, yet?Chipmunk was definitely one of my guesses.
Do you think a chipmunk would be active after dark? My dog doesn't normally react unless he knows that something is right there. I thought chipmunks were mostly active during the day, but I could definitely be wrong about that.
Putting flour around the burrows should help solve this mystery. I hope!
I have similar holes in my yard, but think they're from squirrels...except they're so symmetrical!
I also have moles, and small critters I think are shrews.