Probably because you've got 3 set of parens, so:

$1 eq "[include]";
$2 eq <whatever path you wanted>
$3 eq "[/include]";
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and your s/ would replace all of it by $include. Did you want:

$ThePost =~ s/(\[include\])(\S+?)(\[\/include\])/${1}$include${2}/ig;
or:
$ThePost = "[include]$include[/include]";
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This won't work for multiple [include][/include]'s in the same ThePost, though the first might. Guess I'm still not clear, I thought you wanted to replace the include tags w/ the ssi #include instruction for the filename found between the tags. Don't see why you want to put your [include] tags back in to the output stream.

a