What synth/sampler are you using to add the extra beats?
One possibility is that you need to enable/disable delay compensation for the VSTi that is providing the kick drum, although that seems unlikely as the MIDI is occuring after the audio.
It is also possible that the conversion from mp4 to wav has altered the audio - some algorithms insert silence or mute the initial several milliseconds of audio. Have you zoomed in as far as is actually possible on the audio track to see if the audio lines up with the beat? You can zoom quite a bit.
The only time I've had an issue with that large an offset, a sixteenth of a beat, was trying to use the default wavemapper/wavetable output on a MIDI track. If you haven't assigned the MIDI to a VSTi or external synth that could also be the problem.