framedump at variable framerates

i got a movie, with frames of different durations.
(framereport gives alternating values at different positions in the
movie.)
i need to convert it into a mov (to create an alpha-channel)

doing this with framedump (nonrealtime mode) the duration
of the frames get evenly mapped in the whole movie.

is there a way to do this conversion without loosing the time-
information
for each single frame?
(realtime mode is not an option.)

thanks for any hints
klaus