In the Quartus® II software version 12.1, you can compress the configuration bitstream. However, if you are also using Configuration via Protocol (CvP), compression of the bitstream is not supported.
If you enable CvP for your design and also enable compression of Partial Reconfiguration (PR) bitstream, the PR state machime may not work correctly.
Avoid turning on both CvP and PR compression in the Quartus II software. Use uncompressed bitstreams for designs using CvP with PR.
This problem is fixed beginning with the Quartus II software version 12.1 SP1.