Hmm.
What should be happening is this:

1. You try to execute "myperlscript", which is an executable file, which begins with #!/path/to/my/perl.
2. The system sees that the file begins with #!/path/to/my/perl, and executes /path/to/my/perl with the full path the script as the first argument (and any additional command line arguments will follow)
3. The /path/to/my/perl program (the ksh script) is another text file -- the OS opens this up, sees that it should run /bin/ksh (from the first line), and effectively runs  /bin/ksh /path/to/my/perl myperlscript <args>
4. Now /path/to/my/perl is executed, and its last line is exec /path/to/proper/perl "$@", so it executes /path/to/proper/perl myperlscript <args>
5. perl takes over from here and runs your script...

If your perl script is being executed via ksh, that sounds to me like your wrapper script has an error of some sort -- the wrapper script should be explicitly executing perl on your perl script.
If you post your sample scripts (your perl wrapper and your sample perl script) that will help us diagnose what is happening...

--JAS