Yep, transparency in illustrator... Most likely from applying effects within illustrator (Drop Shadow, Outer Glow, etc.)
I came across a fix for this a while back... I was experimenting with profiles after just having some repairs made to our printer. I noticed that in Wasatch there is an option for ICC input profiles. The is an option for CMYK Vector and Raster and there is also an option for RGB Vector and Raster.
Ours was setup by Mutoh for CMYK Vector: Relative Colormetric / Raster: Perceptual. From what I've found it is basically how the rip interprets CMYK vector files vs. CMYK rasters files. By changing the CMYK Vector to PERCEPTUAL. It corrected the problem.
From test prints that I've made it looks like when a file, that contains transparency, is embedded within a vector file... The rip interprets the vector image separately from the raster image. I would bet that if you check your ICC input profiles within your rip software you would see that your CMYK Vector and Raster setting are different. Setting them to the same, Perceptual should fix the problem...
I know people usually don't wanna get into to changing up profiles, but if you do decide to try this to fix your problem please let me know how it worked for you. I have posted this fix before, but to my knowledge no one has attempted to do it. I'm just curious to see if this works for others.
Same would go for RGB files... I'm only assuming that your printing in CMYK