PLL Reconfig IP currently checks the IO PLL lock status before it allows reconfiguration to start. This causes the mgmt_wait_request to be asserted until the IO PLL achieves lock.
To work around this problem, edit the .v file shown below in the project IP-generated folder and change the parameter WAIT_FOR_LOCK value from 1 to 0. This will force the PLL Reconfig IP to not check the IOPLL lock status and de-assert the mgmt_waitrequest signal when the core is ready.
//synth/altera_pll_reconfig_top.v