Stratix V full reconfiguration only works conditionally

On my Stratix V board, the ability to do a full reconfiguration of the device by asserting !nCONFIG is dependent on the state of the device.

I have never seen this before, nor seen it documented.

The 5SGSMD3E2H29C3 is connected to an EPCQ256 in a x4 configuration. Powerup configuration works in all circumstances.

My design also implements a avalon serial flash controller to boot the Nios from EPCQ. The Nios boot from EPCQ also always works on powerup.

The following seem to prevent reconfig from properly executing:

1) Configuring the device in x4 mode. When this is done, only powerup config works. x1 configuration must be used for reconfiguration to reload from EPCQ

2) If the Nios is allowed to boot from flash, reconfig won't work.

If boot is inhibited by asserting reset while powering up, reconfig will work, repeatedly. Once reset is released and the Nios boots, reconfig stops working.

It appears that it is maybe the boot copier that is the problem in situation 2. With only the FPGA image (sof) programmed in flash, I can load my .elf with the debugger and run it, and reconfig still works.

Quartus II 13.0 with SP 0.23 and 0.24

Edit: Once the device is in the 'bad' state, reloading the .sof via JTAG while holding reset DOES NOT re-enable reconfiguration. So there is some state in the device that is not affected by an sof load.