What if you try to read both the files in some variable, while you're opening the files you specify the Greek encoding for them in the open argument?
Something like; 
#this is Japanese...
my $file = 'unicode_8859_11.txt';
open FH, '<:encoding(iso-2022-jp)', $file  or die "$!\n";

[download]
I know you are dealing with .csv and .xls but I hope my suggestion can offer some light. Excel files are not easy to handle with the Spreadsheet::WriteExcel because they're tab-delimited, a representation of the tab can trickle in the output, this might be why the excel file is giving you troubles, I'd rather convert the file to .csv or convert both files to .txt so handling them becomes easier and such unexpected behaviors kept in check. Make sure you save a copy of the original file.

In addition check this, they got some links to SpreadSheet examples for dealing with foreign languages in Unicode to the left of the page, it might be of use. I wish you luck...

Another point, using the OLE module is recommended over Spreadsheet::WriteExcel for more reliability working with Excel on Windows. Update after reply from jmcnamara

Update:Added a brief idea about Excel tab-delimiters and also about the OLE module

Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.

In reply to Re: WriteExcel unicode question by biohisham
in thread WriteExcel unicode question by demis

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