I created several FLV files in Adobe After Effects from a batch of 600 PNG's and are 20 sec long in run-time. The videos are to be used in Prezi and this is also the way in which I test them. In the hope to reduce the lag that I was experiencing, I made multiple FLV's. Each with their own bit-rate and also on a couple of them I used the same bit-rate but with different format options.
On each FLV there is a slight difference in how smoothly they run but in the end they are all choppy at some point.
Also maybe important to note is that the video backgrounds are transparent, fairly small in file size (less than 12 MB) and run more smoothly on my employer's laptop than my pc when using Prezi.