TM4C1294NCPDT: 5ms period spikes of duration on 5v ( and every where else) on tm4c1294 launchpad from ethernet phy

I am using an external 16 bit a/d to sample an analog encoder and the signal is being affected by large 1us noise spikes every 2.5ms/ 5ms ( there are larger ones every 5ms and they alternate with the 2.5ms) on +5v and everywhere else on the tm4c1294 launchpad, even though I have separate supplies for the launchpad and the analog encoder. When I stop the SYSCTL_RCGCEPHY_R Phy clock, the noise goes away. When I turn off the phy clock to get a reading and turn it back on again, it takes about 1.75 seconds to be able to use the ethernet again. I have tried other registers SRPHY, EPHYSCR, EMACCFG to try to stop this but they haven't worked. Is there any way to stop the phy clk without a long recovery time or a better way to stop the spikes?