--- Quote Start ---
Yes, the sub-compiled partition is encrypted source files. I'll run it on 9.0 ans see if teh problem persists.
thanks
--- Quote End ---
I had the same problem with 9.0
Here is the response from Quartus tech support
////
Proper license information is required to compile encrypted IP cores. The license assignment is imported in to the top-level project when a design is imported as a .qxp file. However, the license assignment contains an absolute path to the licensed IP source files. Therefore, the .qxp file works correctly only if imported into a top-level project on the same computer as the lower-level project, or the IP files are installed in the same directory path location on both computers.
To avoid this problem, you can include this partition in the top-level project instead of importing it, because IP cores generally do not require additional changes by a designer in the project team. You can set the partition that contains the core to Post-Fit after the first compilation to reduce future compilation times, because the partition will not be changing in any subsequent compilation. You can also set the partition to Empty to exclude the IP core from the database until you are ready "
/////
Instead of the suggested workaround, I just edited our automated build scripts to copy the files to the path that Quartus is looking for and removed them after.