This might be easy for you remember.

Whatever you are using in your split use it in your -F as is

for example

perl -naF"/\^/" -e '$key="$F[0],$F[1],$F[2],$F[3]\n"; print $key if ( 
+! $seen{$key} ++ );' datafile
4363,7619082,309839685,309841122
[download]

Notice the -F uses whatever is in your split.

Update: Please quote your param for F switch as you don't want the shell to interpret your backslashes.