PLL Reconfig IP currently checks 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 core is ready.
//synth/altera_pll_reconfig_top.v