Is there a known problem when examining an EPCQ device for the first time when using the Quartus II Programmer version 13.1?

Yes, due to a known problem in the Quartus® II software version 13.1, when the programmer performs an examine on an EPCQ device for the first time the data read back from it may not be as expected. 

This is because the first time an examine is performed, the flash is busy writing to the Non-Volatile Configuration Register (NVCR). This results in the first portion of data read back being empty but the remaining data read back being as expected.

The second time an examine operation is performed, the programmer is able to read back the correct contents from the EPCQ device as the NVCR is no longer written to.

This problem is fixed in the Quartus® II software version 14.0.