I know you're a good coder, so you should be able to figure this out, but if you need help, let me know and I'll do my best to explain. Additionally, I might be able to do better if I could also see your dialog code.
Code:
on *:TEXT:*:#FFXVI:{
  if (FFbot isin $nick) && ($did(systok,28).state == 1) && ($len($5) == 32) && ($1 == Sys) {
    var %sys = $findtok(06 46 93 96,$3,32)
    if $2 == Dow {
      if %sys {
        if $($+(%,sys.dk,%sys),2) != $5 {
          .write backup.txt $($+(%,sys.dk,%sys),2) $date(mm/dd) 
          $+(%,sys.dk,%sys) = $5 
          did -rab systok $gettok(3 11 39 40,%sys,32) $($+(%,sys.dk,%sys),2)
          echo 4 -a $5
        }
        else {          echo 3 -a $5        }
      }
    }
    elseif $2 == UpT {
      if %sys {
        if $($+(%,sys.bk,%sys),2) != $5 {
          .write backup.txt $($+(%,sys.bk,%sys),2) $date(mm/dd) 
          $+(%,sys.bk,%sys) = $5 
          did -rab systok $gettok(12 13 14 15,%sys,32) $($+(%,sys.bk,%sys),2)
          echo 4 -a $5
        }
        else {          echo 3 -a $5        }
      }
    }
  }
}