What version of Lightroom? How are you doing the time-lapse? Using one of the presets you can find online? I have seen this before when I still made time lapses in Lightroom and it is usually related to the framerate in the preset and the export format being different.
P.S. If you have Lightroom through CC, there is a far better and more controllable way to make a time-lapse from a series of images in Photoshop. This also allows you to do 4K video which Lightroom can't do.