I know this is an old thread, but I found a solution for this. I was getting bad RBF files using bitstream compression for my Stratix II part when I had told the main Quartus software to generate the RBF files in the settings checkbox. If I instead generated the RBF file using the commandline tool, the problem went away. Here's how to do it.
Make a file, call it "options.txt", put this one line in it
BITSTREAM_COMPRESSION=ON
Now run this commandline
quartus_cpf -c --option=options.txt Project.sof Project.rbf
This worked great. I've not tried making a POF file in this manner, but quartus_cpf allows you to do that, too. Just type "quartus_cpf -h" to get help on how to do it.