After some trial and error, it turns out guys were right.
There is no strict need of a .bat or .exe file.
The problem was as mentioned in my last post. Windows couldn't run them from any other directory than C:\Perl64\bin .
What I did was a simple workaround. I first make my scheduler to change directory to C:\Perl64\bin and in the same command I run tap.pl. Oh and I'm using "at" command btw.
$status = `at 3:09 cmd /c cd C:\\Perl64\\bin&tap.pl`;
It works. Further discussion/suggestions are welcome.