To clarify japhy's instructions, you want to make just one of the following changes -- either this:

### First I read from database.

$data_path = "data/mixed.data";
open(DAT, $data_path) || die("Could not open file!");
@rawdata=<DAT>;
close(DAT); 
chomp @rawdata;  ## <<-- add this line here
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or else this:

###  Then I overwrite mixed.data with

$data_path = "data/mixed.data";

open(O, ">$data_path"); 
print O @scale;    ## <<-- don't use 'join "\n",...'
close(O);
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Either one alone will fix the problem. (Don't do both.)

update: I should point out that the first solution will work equally well with your initial test case (setting $now,$nill,$null to internal time values, instead of reading them from a file) -- chomp only removes the input record separator (value of $/) from the end of whatever string(s) you pass to it; when a string does not end with with that value, chomp does not alter it. Meanwhile, just doing "print O @scale" will do the wrong thing if the array elements don't end with newlines.