My experience has been that the first row is where the controls (down arrow)
appear when autofilter is invoked. But I've now been sent a spreadsheet (just
unformatted data in a large table) where the autofilter chooses the second
row. I've compared the new spreadsheet with previous versions and don't see
any difference in layout, etc.

What can be causing this problem? Is there something "invisible" that tells
Excel which is the header row for the data to be filtered?

If I select row 1 and then click autofilter, the controls do appear on row 1
but otherwise it's always row 2 in this spreadsheet.