There are several ways Perl can connect with a SFTP server as, for instance, running the external binary directly, using a module that does so or using some modules implementing the SFTP and/or SSH protocols.

The easiest way to know what it is doing is to look at the program source code... if you are unable to do so, just grep for "sftp" over it and post here the output (though, you may like to remove sensible information first).

Another option is to run the program with some utility as truss, to see what is going on at the OS level. You will be able to see if it is running some external program and which Perl modules it is using.

Update: In any case, have you just tried including the directory containing the newer SFTP/SSH binaries in $PATH before calling the Perl program?