That's the point where the problem starts..
If you check the custom category, the format you used when you used comma for both separators , even for currency, is saved there... it will look like : [$$-409]#,##0,00 for US dollars. Means that every time you use currency format, excel will use this custom format.
You should delete this format from the list, otherwise this is the format excel will use when you format to currency.

You should learn more about formatting before saying that "Nothing you said is relevant". From what i see, you understood nothing from what i said.

Just go to advanced options, use different separators for decimal and thousands, then in the custom formats list, select the wrong formats and delete them so they will not be automatically used to format the currency .