This works... I'm not sure what the "%"s in your regex were for.

#!/usr/bin/perl

$text = "<!--begin-->this is a line of text<!--end--><!--begin-->anoth
+er one<!--end-->";

@lines = $text =~ /<\!--begin-->(.*?)<\!--end-->/g;
foreach (@lines) {
  print $_ . "\n";
}
[download]

Peace!
LassiLantar