Unless you have a good reason for not doing so, always use strict in your code

There are several errors in your code:

• While processing file2 and file3, you are using the literals key2 and key3 as hash keys, instead of the variables $key2 and $key3
• While processing file3 and file3 you are incrementing the values of the hashes $hash{key3}++, don't know why
• Also, when processing the files you are assigning different values to the same hash key:

  $hash{key2} = $value11 + $value1;
  $hash{key2} = $value22 + $value2;
  [download]

  the second statement overrides the first. You should be using different (sub)hashes for each value:$hash{$chrX}{value1} += $value11 ...