I tested the following code in #mIRC with version 6.1 and it seems to work fine. It's the same code you posted before just moved to more than one line. You may need to double check that you do not have another on join event interfering with this.

Code:
on *:join:#mIRC:{
  if ($nick(#,0) > %highestPeeps) || (!%highestPeeps) {
    set -s %highestPeeps $nick(#,0) 
    set -s %highestPeepTime $fulldate
} }

Code:
* Set %highestPeeps to 52
-
* Set %highestPeepTime to Thu Feb 19 18:58:51 2004
-
* Set %highestPeeps to 53
-
* Set %highestPeepTime to Thu Feb 19 19:01:57 2004
-
* Set %highestPeeps to 54
-
* Set %highestPeepTime to Thu Feb 19 19:02:10 2004