I can't find anything in cperl-mode that would do this. Try starting emacs with no customizations:
$ emacs -q
and then turn on cperl-mode in the scratch buffer:
M-x cperl-mode
Paste your text; it should look like the original (i.e. all on one line). Then start customizing cperl-mode:
M-x customize-group<RET>cperl<RET>
setting each variable individually for the current session only, and trying the paste in between each setting. If you suddenly find the behavior you're seeing, you have a starting place to look further (it could be a combination of options).
If you get cperl fully customized and it still doesn't behave "incorrectly" then you need to start looking at what other packages could be causing it. It could take a while....