Very slow encoding after upgrade from 5.03 to 5.5 with MXO2 mini

Hi all.
After upgrading from CS5.03 to 5.5 my encoding now takes 5 times as long. A 2 minute HD Video file would take 2 minutes, and still does on the PC I haven't upgraded (identical almost) but now with CS5.5 it takes almost 11 minutes.
Some explanation....
I create HD MJPEG files on a PC with Blackmagic Decklink.
I transfer these files to an HPz800 which used to run CS5.03 with Matrox Utils 5.1.1.37 and an MXO2 Mini with Max. (Nvidia Quadro fx4800 and 12GB of RAM)
On a Blackmagic timeline HD 1080i MJPEG with filters of Auto Color, Fast Color Corrector and Gamma correction a 2 minute timeline would encode in 2 minutes give or take a couple of seconds.
Now with CS5.5 and Mtx 5.5 an identical file takes 11 minutes to encode to Microsoft avi - Matrox 1920 x 1080i - 25fps.
If I remove the filters (which I need to be able to use) it will come down to 2 minutes as it used to be.....so it seems to be the filters are now slowing things down when they never used to. I have never rendered before exporting. Ever. So this time I tried rendering first and it brought the 11 minutes down to 7 minutes but when taking into account the 4 minutes rendering time I am no better off.
I have updated CS5.5 to CS 5.5.1 and MTX Utils to 5.5 and then 5.5.1 and it makes no difference. Still 11 minutes to decode 2 minutes with three filters, which is exactly what I have always been doing but now it doesn't work....
Can anybody help? or make a suggestion as to why using filters in 5.5 now multiplies the encode time by 5 when it never used to. Everything else bar Matrox Utils on this machine is as it was before the upgrade to 5.5 and as I say my older machine is still 5.03 it can do it all in 2 minutes even with the filters intact.
So have I really spent a small fortune upgrading to make my output 5 times slower. Not happy......

To go further, every single encode that I have done is slower than it was before with CS5.01 or 5.03.
This is odd because going from Blackmagic to any other codec doesn't necessarily need the Matrox box or Matrox utils
Blackmagic HD or SD to
Matrox HD
QT HD MP4
QT SD DV25
DV AVI SD
Mpeg2 - DVD
Every single encode is slow by 2x to 6x.
Why should Blackmagic HD to QT MOV MP4 take twice as long as it used to...... having said that The speeds I am seeing now are what it was like before I attached the box in the first place, whether a Matrox codec was involved or not.... It is acting like a blocked funnel. when it used to be a lovely wide and clear funnel.
Anyway Matrox have reproduced the problem and are investigating, so hopefully there will be an answer soon....

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