Couple of items missing in your description, like disk setup, number of CPU's and the like.
But from what you have given, there are a number of issues here:
1. Matrox is a show stopper and best used for its designed purpose, as a doorstop.
2. ATI Fire does not support hardware MPE.
3. OCZ IBIS may slow down the system.
4. 16 GB is suboptimal for that chipset and slows the system down.
What other disks do you have, what happens when you completely remove the 'doorstop' Matrox alltogether?
We are working with a Matrox MXO2 box and experienced identical issues to yours. This is what helped us after we figures out there is an incompatibility issue between Matrox and Surcode. In Program Files\Adobe\Premiere Pro\CS5\MediaIO rename the file surcodewrapper.vca to surcodewrapper.bak. Do the same for Adobe Media Encoder. Doing this solved all our delay issues, but at the same time it will disable usage of Surcode's AC3 format.
Note, the path to the file is from the top of my head while waiting for my wife to come out of surgery at the hospital, so it may not be 100% accurate. A quick file search in the Adobe folder may serve you better. :-)
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