I just read thru the email thread between you and Jon, that he forwarded me to help figure out your problem. I noticed this attachment, which shows the color/density of your 21 step strip measurements. This visually shows the same thing as your linearizations- dark highlights then regular mid-tones to shadow range. I have again reviewed your ink separation, and edited it to make your paper white match mine for better comparison, and other than your yellow shade 7 don't see anything really obvious that would cause such dark highlights...
How old is this R3000 printer? For some reason, yellow is always the worst for color staining. It's worse with an older printer, as I think the yellow pigment particles collect in the nooks and crannies of the damper. When you flush or print, the surface yellow gets flushed, then more releases while the printer sits, which causes highlights to print yellow again. Without flushing the printer's internal ink lines with PiezoFlush, the only sure way to eliminate color staining is to replace the ink selector unit (dampers), otherwise, printing yellow purge sheets or doing cleaning cycles to get rid of the yellow before each printing session until it no longer appears is the solution.
Please check your QTR version (the version listed at the top of the window is not necessarily the version #). To do this, open QTRgui, then select Help and choose About. The window that opens will list different versions for different parts of QTR, please let me know what version is listed for "Quad to Printer".
Have you deleted and reinstalled your print driver and QuadTone RIP?
Another thing I would check is ink in the carts, removing the printer and printing process/settings from the equation. To do this, get some Q-tips/cotton swabs, and a piece of coated inkjet paper (a scrap piece from a bad print is fine). Shake your carts well, then line them up from shade 1 to 7 (black to yellow). Dip the end of a Q-tip so it's wet with ink, then gently wipe it across the paper surface to make an ink smear. Mark the smear with the cartridge position/ink it came from, then use a new Q-tip to test the next ink, and continue until you have a sample smear of all inks. I have included an example below for you to see what I'm talking about.
Please let me know, thanks~ Dana