Hello,
I have got exactly the same problem.
I see, you have got Canon C4580, we have got IR C4080. Exactly same output - bitmaps in PDF disorted.
It happens with PostScript driver, not with UFR driver.
What I have tested:
1. All available Canon PostScript drivers (4.7, 4.8, 4.9, 14.00), no joy.
2. Win7 / WinXP 32bit / 64bit - no joy.
3. Canon serviceman - He says, there is no newer PostScript firmware for this device - no joy.
4. We have got new Canon C2025 now - there is different PostScript module - it prints these suspicious PDFs just fine!
Conclusion: I guess there is something new in PDF in InDesign CS6, which is not going well with Canon ImageRunner machines with some particular PostScript module. Fiddling with PDF I have found it has something to do with CMYK profiles.
Jan