I'm having the same problem here.
Designing in Illustrator CS2, and RIPing in Flexi 7 Production Manager on a Mimaki JV3-160SP.
Here are the results of printing transparencies:
Here's a link to the eps:
http://www.sendspace.com/file/ytyn1o
Illustrator is using the US Web Coated (SWOP) V2 CMYK profile, and Production Manager has the same CMYK profile for input. I'm working in the CMYK document mode. I've tried many things to fix this, from trying almost every legacy format of eps/pdf/ai to testing an ONYX trial (Onyx experienced the same problem). I did not have a problem printing the same document on my old Roland printer through their versaworks software, however that is no longer an option. After talking with SAi, I was told that the problem was with how Illustrator outputs the documents. They anticipate a fix for Flexi 8 at an unspecified time and do not plan on fixing the problem in Flexi 7.
Alternatively, can anyone recommend better software for just a RIP and/or cut solution? Currently I design in Illustrator, RIP in Flexi, and cut in SignLab. I would like to design in Illustrator, as it's excellent for that, but need to replace the other software. The SignLab software I've tried has been pretty horrible in almost every aspect, though we only use it for cutting.
Cutting still mostly works for us, so finding a proper RIP solution (or fixing Flexi 7) is the priority. Something with decent cutting abilities would be a nice bonus.