Hi John,
I did some WDM simulations of Pop III star formation quite a while back (~circa 2006), but I never saw anything like this. One lesson I've come to appreciate is to try to identify whether the problem is with your initial conditions or with Enzo itself - for cosmological simulations with highly nested grids/particles, all sorts of weird things can go wrong.
One particularly entertaining problem is if you've made the nested regions too close together so that a very massive particle ends up in the refinement region - given the way the gravity solver works, the mass from a particle is deposited into a small number of cells on a grid so you can get massive particles causing all sorts of odd effects. That's the first thing I'd check - do you have any massive particles within the virial radius of your halo?
The second thing I'd do is check the initial conditions at high redshift to see if something funny is going on. Do the particles have sensible velocity and displacement distributions? MUSIC is known to occasionally do very strange things when generating initial conditions, so if you're using that you may wish to either examine the IC files directly or look at the first data output to see if something strange is going on with your initialization.
Otherwise, please feel free to send your Enzo and IC generator parameter files around and we'll take a look!
--Brian