You had the capacitor where the bypass diode would be on my diagram right? All 6 turbines are of the same voltage?
You made sure that you did not wire any of the capacitors backwards right?

Because that would explain the stalling.
Try an add the bypass diodes, because that way the bridge rectifier is not conducting at all when a turbine is stalled. And since this only seems to happen with only 3, I would test different combinations to make sure that it is not an issue with a specific turbine or rectifier or something is miswired.
You had the capacitor where the bypass diode would be on my diagram right? - yes, electrolytic capacitor, with correct polarity
All 6 turbines are of the same voltage? -> yes , all 48V
You made sure that you did not wire any of the capacitors backwards right?

Because that would explain the stalling. >> yes I checked several times
Try an add the bypass diodes, because that way the bridge rectifier is not conducting at all when a turbine is stalled. And since this only seems to happen with only 3, I would test different combinations to make sure that it is not an issue with a specific turbine or rectifier or something is miswired. >>>> yes, I will have to by separately single diode, probably you say that current will pass through a single diode insead of having to go through 2 in series from rectifier bridge.
I still can't explain this behavior. I have started to configure advanced controllers for each and add all of them in parallel, because I have noticed that if you add the same load in amps to all of them, the wind turbine that has highest RPM will continue to increase the RPM at the same load and as the MPPT increases the load as the voltage rises, the ones with highest RPM continue to increase and the ones with low RPM will have lower and lower RPM and this might be conclusive for me that it is not possible to have all of them in series without series side effects like too high rpm, magnets damaging, blades get broken...
I have controller with 5 point load that i will add one for each wind turbine and configure the points of load based on RPM and not voltage.
See all settings I have for the wind controller.