The "timers off" was the problem. It would be better to give a unique name to each timer for each nick. Also I made the timers & /notice command silent. Try this

Code:
 on *:SNOTICE:*client connecting*:{
  .timer 1 5 .ctcp $4 version
  $+(.timercheckver,$cid,$nick) 1 15 .notice $nick I did not get a version reply from you
}

on 1:CTCPREPLY:VERSION*:{
  $+(.timercheckver,$cid,$nick) off
  write versionlog. $+ $asctime(yyyy-mm-dd) $+ .txt $2-
  if ($read(versions.txt, s, $2)) wallops Version Alert for $nick using $2- $read(versions.txt, s, $2)
}

If you have a plastic floor runner over your tiles, then you're one Hella Pinoy!