Thanks Bill.
Several times, i tried various animated gifs, howeever only the first 2
seconds would play. The gif would then just stop. Perhaps the raason was that
there were too many frames per second ( 25) and at 14-15 seconds ( 320 x 240)
the gif renderer in powerpoint may have been unable to keep up...

I tested these transparent Gifs in a browser and they seemed to work quite
well.

So, i have taken the long way around the problem.

For others having the same problem, one clunky workaround is to layer a copy
of the background image being used in Powerpoint into the same program that
you are using to create your transparent animation. So, if u are using After
affects or Premier or other applications, put/composite a screen copy of the
powerpoint presentation frame behind your animation - the same animation that
has the transparency.
Then create a video specifically of the rectangular region of interest and
import that vicdeo and very carefully layout it over the presentation frame
so that the background of the video matches the background of the
presentation.

Hint: When you select the size of your region of interest, try to use a
width height ratio of 4:3 or something else pretty standard, because if u
dont many of the video comopression codecs may refuse to create a video file
with an odd ratio, and that will leave you with only the option of using
uncompressed video which can be huge.

Region of interest is an aferaffects term which means selecting the area
with a marquee and pottentially cropping it later, as one would do in
photoshop or psp.