The best way to encode your video files is to export your work into a production codec (ProRes, DNxHD or uncompressed, for example). Then, use the open source tool Handbrake to convert it into an mp4. Make sure to use h264 as codec, otherwise the video will be software-decoded and might stutter.
The startup video should be shown with the markers visible in the corners. If you cannot see the markers, there is some cropping going on. Also, depending on your setup, you might hear the startup sound of an old projector.
You can make changes to the config.txt on the boot drive for setting options or to force certain video modes. This can be useful when the display or projector is incorrectly, or not at all detected.
The boot partition should show up on your computer after writing the image, or when you plug in the card again. Open the file config.txt with a standard text editor.
Overscan / Clipping / Cropping
To adjust the image by moving its borders inwards, replace “disable_overscan=1” with
disable_overscan=0 overscan_left=1 overscan_right=1 overscan_top=1 overscan_bottom=1
Increase the Values on each side until you can see the markers properly.
For example, add
hdmi_group=1 hdmi_mode=16 hdmi_force_mode=1 hdmi_force_hotplug=1
to the config.txt which will force 1920×1080 at 60hz. Or
will give you 1920×1200 at 60hz.
These setting will prevent the Pi from figuring out what resolution to use, but use the given video mode.
Find complete information on video modes and options on raspberry.org.