The Feedback Clock for the QSPI Flash Memory on the MicroZed needs to be selected and assigned to MIO8 for the QSPI device to operate correctly. The MicroZed 'preset' in Vivado 2013.4 assigns this correctly but MicroZed preset in Vivado 2013.3 does not.
If you are building a MicroZed design in Vivado 2013.3 you will need to manually set the QSPI Feedback clock and make sure it is assigned to MIO8.
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-Gary