I am keying from the behavior you identified with a customer-supplied pdf. You probably have your software set to keep the color profile of imported objects. So when the color prints right on that imported object but not on objects you create de novo, that tells me the problem lies in your native color export profiles. At least that's what I'm guessing.
If you want some advice, it will be faster and more direct (and cost less in the long run) to just buy or build a new computer, install the new version of Onyx, and use that, also going to the trouble of building profiles for your media if you have the ability. Onyx has built-in conversions for more accurate printing of Pantone colors. And you can eliminate the use of Flexi, exporting your print files directly from Illustrator, and importing to Onyx. When you use Flexi as the intermediary, you introduce the possibility of more color errors because every time you import and export an object, the software applies a color profile to it (think of it as a "correction"). You can get a passable computer for $600-800, and a really good one for $1000-1200. It doesn't take getting stalled over color problems in very many jobs before you wish you were able to use the RIP Epson recommends and not have to pass through two design softwares.