I would peruse perlrun and use some switches to eliminate much of your setup. Also, I'd use timelocal instead of mktime.

perl -MTime::Local -nle 'if(/^(\d{4}-\d{2}-\d{2}\s\d{2}:\d{2}:\d{2}),(
+\d{3})/){ $o="$1$2"; @a = reverse split( "[-: ]", $1);$a[3]-=1;$a[4]-
+=1;$a[5]-=1900; if(!$l){$t=localtime(@a,0,0,0)*1000+$2; $l=1;} else {
+ $t2=localtime(@a,0,0,0)*1000+$2;$e=$t2-$t;$t=$t2;$l=0;print "$o $e\n
+";}}'
[download]

This makes your code a bit shorter. Personally it still feels too long and I would put the code into a script.

Update: I first had localtime instead of timelocal...