According to the VESA DMT standard, the 1280x800x60p video mode should be output to monitors using a vertical frequency of 59.810Hz, which is significantly slower than the 60Hz at which your video is encoded. This difference in speeds causes the video output to run slower than the video decode at the rate of 1 frame every 5 seconds, resulting in the dropped frames seen on screen.
This discrepancy can affect other VESA modes to a lesser extent. The following modes may exhibit a dropped frame once every 8-10 seconds: 1400x1050x75p, 1440x900x60p, 1680x1050x60p, 1920x1200x60p.
Because the frequency discrepancy is part of the standard, this issue cannot be fixed. If you wish to avoid dropped frames with your video, we recommend doing one of the following:
Downscale the video to a TV mode at 60p (e.g. set the video output to 1280x720x60p).
Upscale the video to a TV mode at 60p (e.g. set the video output to 1920x1080x60p).
Re-encode the video so that it uses the exact refresh rate of the VESA mode (for example, 59.810Hz for 1280x800x60p). This is the only way to fix the dropped frames problem without changing the resolution. Note that this will cause video playback to be slightly slower, so any accompanying audio will need to be matched to the new refresh rate as well.