For a filter command to work, we do need at least one "title" cell at the top. You're saying that you actually have two?
The code section "get a temporary list of unique values" is copy all of column A to column EE. If the resulting list in EE includes a value in E2 you want excluded (we have to leave E1 in as a "header"), then let's just delete that cell before proceeding. Edit this section:
If this doesn't help, post up a usable example workbook so we can look at the problem directly together.
Click GO ADVANCED and use the paperclip icon to post up your workbook.
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