Hello,
KMIN and EMIN should remain small and are used just to prevent K and epsilon to become negative, this should be uncoupled from initial or boundary conditions. You can put at the entrance a turbulence that corresponds to turbulent energy being a percentage of the total kinetic energy (this is hardcoded in kepcl3, see the parts of code that are commented out, proposed as an alternative to EBORL=EMIN and KBORL=KMIN).
I would suggest that at least you use hardcoded values at boundary conditions and/or initial conditions, 1.D-3 if you want, but not through ELIN and KMIN, letting EMIN and KMIN at their smaller values. I do not believe too much in the effect in initial conditions (they will go away with the flow) but more in boundary conditions.
Think also that NUT=CMU*K**2/E, so that EMIN=KMIN=1.D-3 gives only NUT=9.D-5, it is not so high at the entrance...
With best regards,
Jean-Michel Hervouet