The MPPT unit is probably drawing current from the turbine that produces the higher voltage, and as both turbines are connected via diodes the lower voltage producing turbine can't forward-bias its diode so can't contribute much current at all.
The MPPT unit will be maximising the voltage at the turbine, ie it is keeping the turbine DC voltage high. It's like the effect of both turbines going through their diodes into a large cap, the cap will be charged to the voltage of the higher turbine, then the lower turbine will hardly contribute at all.
There's no easy way around this, the 2 turbines will probably always produce different voltages and different output power, you really need 2 MPPT units, or no MPPT units so the turbines are tied to a low voltage load.