Hope this helps you zero in on the issue..
I am experiencing a similar problem and tried disabling Java. That did not solve my problem. Something causes Adobe to not see any printers as being installed. Once this happens, I am unable to print from any application until I reboot. I am using Reader 9.3.4 on Windows 7 64-bit.
P.S. If you see a Yellow Message Bar anytime, while opening any PDF, please make a note of the same.