It is a bit suspicious that a patched TA exhibits this behavior while an unpatched TA does not, but I'm still fairly positive it has something to do with the new things that TA does (in this case it would seem to be an option that was disabled by default that is now enabled by default; see below).
Original post follows. Maybe you've tried all of them already-but I can't know that.
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TA has some options that DA doesn't have-as well as some options that DA does have, but that are on by default, instead of off.
The first thing I would suggest is to disable anti-aliasing, or lower it to 1x, whichever you prefer. I have never understood why 4x AA is a default setting in GCII, given that it is in theory supposed to be able to run on lower hardware (which obviously enough would have trouble with that).
The second thing I would sugggest is to uncheck Use Enhanced Ship Rendering. I believe that's enabled by default. Allow Mixed Vertex Processing Mode should be disabled by default in the latest TA, but check on that as well.
You might also consider running windowed rather than fullscreen. It's possible that your video card has trouble with the animated components, but I don't have enough information to know for sure. In any case, it's worth unchecking Enable Animated Components.
Those are essentially the "new" things in TA...the only other things that come to mind would be Disable Bump Mapping and Disable Point Sprites, which may or may not solve the problem, or even help for that matter, but if DA runs fine then those two should not be the issue.
It would help to know the exact specs of your system-for instance, there's a big difference between a P4 @ 2.7GHZ and a C2D @ 2.7GHZ. My assumption is that it's not overclocked, which narrows the field a bit, but you still haven't provided that much information. However, your video is more important than your processor in this case-even if it's a Pentium 4-and not knowing what that is is definitely a roadblock to helping you. My educated guess is that you're running on 845G or 865G, which are both somewhat limited in the things that they can do (and so when TA tries to tell them to do something they can't, they go batshit insane).
Go to Start-->Run and type in msinfo32. In the System Information window that loads, go down to Components and then within there Display. The Name field there should tell us what your integrated video is-if not that, Adapter Description.
Alternatively, you can get this information from right clicking on My Computer, selecting Properties, clicking on the Hardware tab, clicking the Device Manager button, and looking in Display Adapters.