Can you post before and after screenshots? That will help us figure out what's going on.
You're probably running into what we call "pixel alignment" issues.
AI supports very precise sub-pixel object placement because it can output to print (where pixels don't really matter). However, these objects look blurry when displayed on a computer monitor (where pixels do matter). You can see this simply by drawing a rectangle in AI at 100% zoom. Objects in FC must be aligned on pixel boundaries because it exclusively outputs to a computer monitor. When you import and manipulate artwork, FC automatically aligns it to pixel boundaries. This is good because your blurry rectangle will become not blurry, but it's not so good because small fiddly objects don't look exactly right. That's probably what's happening to you.
The best method for maximizing fidelity is to ensure that all objects are aligned on pixel boundaries in AI. This has some subtleties, so you'll probably have to experiment to be able to do it reliably. The most obvious pitfall that I know of is that AI aligns rectangles from the center of their strokes, while FC aligns them to the edge of the stroke. So if you have a 1px stroke, you may have to place it 0.5px off of where AI would naturally place it.
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Here is a great video that covers pixel alignment in Illustrator as well as other tips on prepping artwork for import into Catalyst:
I'll need to realign things to a grid in Illustrator to ensure more accuracy.
Our team wanted me to play with Catalyst and see if it will be viable for our Flex development. I like the application so far - I just really wish it was out of Beta. I am running Vista 64bit, and with this comp, Catalyst takes a whole gig of memory. Optimizing graphics seems the best way to go.
Thank you for your help!