I just upgraded to Premiere Pro CS5.5 from CS4 today and I'm encoding an FLV file. CS5.5 is taking twice as long as CS4 did. I've been creating a weekly video for the past two years in CS4 and encoding it took an average 4hrs for a 10-15min video. I'm encoding the same vidoe on CS5.5 and I'm at 7.25 hrs with still another 45 minutes left. I thought it would be faster. I'm on a Sony VAIO with 8GB of RAM; which I recently upgraded from 4GB. Did I do something wrong?
First off, encoding should be at least 20% faster I'd say, with the improvements made since CS4. I don't know about FLV encode specifically, so there may be some fudge factor there, but taking twice as long doesn't make sense. To ensure an apples-to-apples comparison between your CS4 & CS5.5 encodes, look for things like added effects and specific FLV encode settings you may be using. You might have to turn over some rocks to find some setting that is slowing you down since you may not be that familiar with some of the new options and look/feel of CS5.5.
Checking Maximum Render Quality can slow things down dramatically.