The FF7 field script sets a number of frames to count and soon after calls the movie. Once the frame count is up, the script resumes when the movie is expected to stop. If the frames exceed or fall short of this frame count as called on by the field script, then you experience oddities. Aali can possibly come up with some wizardry to bypass it, but one solution would be to bundle the FMVs with different frame rates alongside field files to insert that have been modified to accommodate them. This can be done in Meteor and fortunately is none too difficult, however the downside is that modifying the field files will make them incompatible with any other mods which alter them. On the other hand, you can always make compatibility patches down the road so it's not too big of a downside.
As an example of the potential for this, a project I was working on before I got tired of Meteor's slowness was to completely modify the beginning cutscene. I had a 30 fps video with the PS3 tech demo train rolling into the station, a prerecorded video of the guards being taken out and Barret waving to Cloud added onto the end of that, and finally the PS3 tech demo Cloud jumping off the train and landing. Field script was modified to start actual game events already on the ground with the prior events already wrapped up.
There are ways around everything.