Description
Due to a problem in the Quartus II software version 13.0 and earlier, using dual-regional clocks in a Partial Reconfiguration (PR) design may result in above internal error when compiling the reconfigurable revision.
Resolution
To work around this problem, use other clock routing resources such as global, regional, or periphery clocks in PR designs.
This problem is scheduled to be fixed in a future release of the Quartus II software.