It seems that all of this fiddling with the $flag could be replaced by a flip-flop operator:

while (<DATA>) {
     ...
    if (/UNX|WNT|COMPONENT/ .. /$target_os/) { ... }
}
[download]

See perlop for details on the flip-flop operator.

But without having a textual description of what your program does it seems hard for me to check if that does what you want.