I can see them.

It looks like there are some significant elevation differences (50 feet or so) for the first 15 miles, and then they match for the rest of the ride. Perhaps the barometer of the altimeter device was correcting itself in that period. You could download the GPX files and verify if you're interested (caution, those files are just lots of text and code)... wouldn't tell you which one is right, but might give some insight into why they're different.

BTW, the difference in air pressure between 1000 ft and 1010 feet is about 6/1000 of a psi - it's amazing how sensitive those altimeters can be, but it doesn't take much of a glitch to get a wonky result.