system("foo.pl","&");
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This calls foo.pl with the character & as its first argument.

system("foo.pl  & ");
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This calls /bin/sh (or your appropriate system shell) and passes it the whole string as command. The shell then interprets the & as a directive to background the command.

The next two are equivalent, but only in the second the shell is involved:

system("foo.pl", "&");
system("foo.pl '&' ");
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