If you change formatting on the cell, this overrides any conditional RowFormat formatting of the same 'type'. For example, if you specifically set a cell to have blue font, this will overrride any .RowFormat format that would change the font colour, but cell background colour or bold/italic font would still work.

FormatHidden is essentially setting the row height to zero. What probably has happened is that you have specifically set the row height and this is overriding the FormatHidden. It's possible that the original testing by setting all rows to FormatHidden has caused the scenario of giving unexpected results now.

Andrew is right that using the ZeroSuppress button in the toolbar is a better (and easier) way to simply hide accounts that have all zero amounts.