You can't build your output string until you've processed all the entries in your files. Replace the print just before your subroutine with

print OUTPUT "$_,$output{$_}\n" for sort keys %output;
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Your file will now contain:

2010-02-12_aaa,1308
2010-02-12_bbb,748
2010-02-12_ccc,316
2010-02-13_aaa,1490
2010-02-13_bbb,1572
2010-02-13_ddd,1704
2010-02-14_aaa,338
2010-02-14_bbb,1508
2010-02-14_ccc,1930
[download]

Your next task is to tidy up your source code, it's a mess :-)

Some hints:

• You use strict and warnings. This is very good.
• Always check that your opens and opendirs succeeded.
• Don't call subroutines using &readfiles(...). You don't need the "&" and it doesn't do what you think it does.
• Pick more meaningful variable names, @files and @files2 are rarely good choices.
• You don't seem to understand the point of calling subroutines with parameters. See perlsub.
• Always declare variables in the smallest possible scope. Coping with Scoping may help (its old, but still worth a read).
• Most importantly, enjoy your Perl programming.