CS5 - publishing AS2.0 SWFs very slow

Having just recently started to work with CS5 I can't help noticing that publishing/exporting SWFs is very slow compared to CS3. A file that takes 3 seconds for CS3 to publish takes, on average, 12 seconds to publish in CS5... 4 times slower!
Anyone know of anything we can do to reduce the amount of time needed to publish? This is a pretty powerful kit - 2.67GHz quad-core CPU with 6GB of RAM so it shouldn't really be having any performance issues!
Or is this just a 'benefit' of 'upgrading' to CS5?!
Any suggestions (other than 'move to AS3.0', thanks!) gratefully received...!

Magnus is correct - here's the relevant info lifted from the MXO release notes:
Adobe Media Encoder
¦ Note If you’re using Adobe Media Encoder with a Matrox MXO2 product that
has the Matrox MAX option, see also “Matrox MAX H.264 encoding (MAX
option)” on page 10.
• When you export a Matrox PAL sequence to MPEG2-2 DVD format using
Adobe Media Encoder, set the Field Order to Upper under Basic Video
Settings in the Export Settings dialog box. Otherwise, your export may
be blurry. (Ref# 51007)
• If you find that switching the export format in the Export Settings dialog
box sometimes takes a long time, such as when you switch from Microsoft
AVI to MPEG2-DVD, rename the SurCodeWrapper.vca file on your system
(for example, rename the file to SurCodeWrapper.vca.bak). This file is
usually installed by Adobe Premiere Pro in the following folders:
$ \Program Files\Adobe\Adobe Premiere Pro CS5\MediaIO\codecs\
$ \Program Files\Adobe\Adobe Media Encoder CS5\MediaIO\codecs\
Be aware that after renaming the SurCodeWrapper.vca file, you won’t be able
to export audio to SwCode Dolby Digital, but you will still be able to export
audio to Dolby. (Ref# 55279 and Adobe Ref# 2603943

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3 Cores with 3GB each: 9:36
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From the initial description this sounds a lot like the problems I've been having with rendering in After Effects CS5.
I have read a lot online about hyper-threading being the cause and have been adjusting various settings with multiprocessing and turning hyper-threading on and off. So far nothing has been able to give me consistent processor use during renders or reliable render times.
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Big Bad MF Mac
12 core Mac Pro, 2 x 2.93 GHz 6 core Intel Xeon, 32GB of RAM.
Boot Drive is 1TB
3 additional 2TB Hard drives RAID 0 for a 6TB Media Drive
Mac OS 10.6.4
After Effects 10.0.1
Project details are:
1920x1080, 23.976 FPS
Footage is all uncompressed 4:4:4 AJA Kona 10 bit RGB captured using Final Cut Pro from a Sony F950.
Project Color space is Apple RGB.
Using Keylight 1.2 to Key video and then placing the footage as a 3D layer, with several other 3D layers with 2 spot lights on the footage to generate shadows on the background layer.
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I'm going to add some more information just in case some engineer at Adobe gets his hands on this. HINT HINT
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