Okay, so I moved it until after WakabaMark finishes messing with the text, and did my best to work around the strange placement of the tags it introduced. Here's my "final" solution (until I get rid of Wakabamark completely and start from scrath):

if($res=~/.*\[spoiler\].*/){
	$res=~s/\[spoiler\]*/\<span class\=\'spoiler\'\>/g;
	$res=~s/\[\/spoiler\]*/\<\/span\>/g;
	$res=~s/\<p\>/ /g;
	$res=~s/\<\/p\>/\<br \/\>\<br \/\>/g;
	$res=~s/\<br \/>/ /;
	$res=~s/\<\/span\>\<br \/\>\<br \/\>/\<\/span\>/g;
}