Hello Edu,
Glad to hear you are doing profit with the USDJPY portfolios.
Now, for EURUSD EAs( I guess the ones from my Portfolio course) you placed them on EA Studio and they were losing but on the MT were profiting. If you are using one and the same Historical data there should be no difference. I mean recalculating the EAs on EA studio and testing them on MT with the same data should give you same results as it gives you in USDJPY.
Simply if there is a difference it should be for all assets and not just for one.
Make sure you have the same settings on EA Studio and MT and the same historical data.