Your original formula was looking at differing range sizes. So in the one instance you're looking at a range down to row 539 and then only down to 296. It's far easier to keep an eye on where these things could be going wrong if your range sizes match.

Also in the first MATCH you are looking at multiple columns where you should be looking at only one column.

Have a read of http://www.contextures.com/xlFunctions03.html . It gives lots of clear information on how to use INDEX & MATCH.

Having had a look again at your formula I an confused as to why you're using the IF(ISERROR approach. Are you just using this to produce a zero if no match is found?

I presume from the number of rows in your example workbook (1million+) that you're using Excel 2007 or later?
If this is the case then you can use =IFERROR() rather than an IF and ISERROR then doubling up the formula. So the formula in F5 and copied down would be:

=IFERROR(INDEX(Citrus!$A$1:$G$56,MATCH($A5,Citrus! $A$1:$A$56,0),MATCH(D$1,Citrus!$A$1:$G$1,0)),0)

Hope that helps. :)