What output style are you using and have you altered it at all? the setting for entering the comma after the author would need to be specified in the Citation template. See the first image attached for the citation template settings you want to change.
(Edit, edit output style> edit “your current style” – then after editing - save as to a new output style. You then need to go to the endnote ribbon and change the output style to your newly named style. Do not name it the same as the original style, or endnote may not know which of the two files that may live in two different places - to use.
I assume that the settings in the second image attached is why the et al worked. you may want to remove the comma there - but I think endnote will automatically resolve a double punctuation mark (like comma-comma) but best to be clean, to ensure weird things don’t happen unexpectedly.
By the way, I would think that a comma before the parenthesis, would be grammatically incorrect. You don’t usually need a comma prior to a parenthetical item?