Exact settings depend on the printer. Most commercial printers these days prefer file transparencies intact. The best setting to use in that instance is PDF/X-4. PDF/X-3 and PDF/X/1a are other choices for commercial print, but both of these outputs flatten transparency.
It is interesting that you don't have problems with digital printing. A common issue is the "Yucky Discolored Box" syndrome. This can occur if you have a drop shadow over top of a vector color fill. When you have this there is raster information adjacent to vector information. Digital presses may treat the raster and vector differently, and sometimes there is an unwanted color shift in the printed result (it's not something you see on-screen).
But if you're having success with the digital printing I wouldn't worry about that at this point. If you need more specific input concerning your file, you might want to post the file or a screen shot so the regular posters here can get handle on the logo problem.
Regarding settings for digital printers, it's best if the printer suggests the settings. Some quick print RIPs prefer RGB input, in which case you would convert to RGB when you output the PDF.
Keep in mind that desktop inkjet and lazer printers do not use a halftone screen. Regardless, any diffusion dither stochastic screening is undetectable by the human eye. You'd see a less than 100% density using a loupe. So, the press sheet does show a halftone screen, unless the press is printing stochastically. Odds are it is not. So, if your logo is 85% Cyan, you'll see a 15% white dot ( depending on dot gain ). Your PDF could very well be setup correctly, but RIP's and PRINTS differently, depending on the output device.
Your Printer should have preflighted your files when they came in to determine if they were of the correct resolution and color mode to print on their equipment. You might consider asking the Printer what resolution their output device for film/plates images at, high end printer will image at 2400 or higher. You might also ask what line screen (lpi or lines per inch) they are using for process color screening, high end printer use 133 to 175 conventional screening or 25µ to 10µ on Stochastic screening. What type of printing presses or printing process are you using, if you're printing a logo to a media like a CD or DVD with screen printing process you may have line screens as low as 55. See you're telling us about the symptom but not about the printers process and what type of services he is providing or claims to provide. Is it a commercial printer producing with large offset presses or small shop with duplicators? What size presses are you having these logos run on, are they flexo, litho, UV, Screen print?
There may very well not be anything wrong with your files.
Thanks to everyone for the excellent information. Using the replies to my post, I was able to have a more intelligent conversation about my issues with 4 color process printing with my printer (who is very accessible & helpful, BTW). I'm confident that they are using industry standard equipment and printing methods. Thank you again, this forum is a wonderful resource for me.