Rendering After Effects Comps can be very slow

I have a PP CS6 project which has quite a few in-line After Effects comps in the main sequence.  The are all image stabilisation (for clips which are are of a different size of the sequence).  When I render then most of fairly quick (several frames a second) but some are very slow (a frame every few seconds).  The settings on the warp stabilise is the same for all of them.  It seems to be the longer clips that cause problems (sometimes over 30 secs). Anyone know why or got a way to speed up the longer clips?


Captain Mench wrote:
Now -- if you need to export an alpha channel out of AE then you'll need some specific formats.
Good luck,
Welcome home, Mench!
To maintain the alpha channel from AE, the OP will want to look up how to be using two codecs, Animation and ProRes 4444. Both are extensively described in the help system for FCP and After Effects or just google them for several hours of interesting reading. The OP will also need to understand the concept of an alpha channel which, come to think of it, was difficult for me.