I was also wrestling with the "PDF printing bold" issue, and had some success when I flattened transparency. But even when I followed all of the "rules" (images on layer below text, all transparent effects rasterized), the text in my color proofs was still getting inexplicably bold, or more accurately: the text looked like it was printed twice- registration was a bit off.
I'm using InDesign 5.5 to make a 20+ page newsletter (mixed images & text). Tried all kinds of InDesign settings, all kinds of Acrobat settings, but the one that ended up doing the trick was buried in the printer's properties dialogue: Simulate Overprinting. When I turned that on, my text came out exactly as intended, and there was much rejoicing.
There seems to be an odd interaction between Acrobat's print dialogue and some printer settings. For example, you'll get weirdness if you try to print "booklet" via the printer's applet (mine's a Canon C7065), but if you use Adobe Acrobat's "booklet" feature, all is well. For my newsletter to print correctly, I have to set a number of items in both dialogues, and in my case the overprint setting was a big find.
Hope that helps!