It may not exactly be that cmd.exe is being called. What you are more likely seeing is a side effect of the way programs need to pass arguments to MS-Win programs. A similar issue (parameter list mangling) was seen recently when someone ran into problems passing parameters from Java to Perl with a system call. He too was passing a list.
The issue is this: MS-Windows programs don't actually get lists when they are called by Ms-Win. They expect to get a single string (lpCmdLine). Programs usually have some internal code that converts that string back into an array. In order to play nicely with that code, Java (and I now suspect Perl) takes your list and concatenates it into a string before passing it. The program (in this case Perl) then splits it back into arguments and viola.
For some in depth discussion about why there just aren't any good choices in this matter, see http://bugs.sun.com/view_bug.do?bug_id=4064116. You might also want to look at these two posts on the Java/Perl thread: Re^9: Running perl from java and Re^8: Running perl from java or the thread as a whole.