use the new release version 1.0.1 of the FX3 SDK there was a bug fix in this case.
Or use these two lines instead of GpifDisable(CyTrue)
memset ((void *) 0xe0014000, 0, 0x1000);
this resets the GPIF configuration at all.
Thank you !
But is it mandatory to force the reload using GpifDisable(CyTrue)? In my application I am using GpifDisable(CyFalse) but then reload the configuration anyway using CyU3PGpifLoad(). So far it is working fine.