Thanks for your reply Genius.
I tried it, and it does work. Just a little spammy though grin

Anyway, I should have tried some more myself, before asking.
Came up with the below alias, and that does the trick for me.
Again, thank you for looking into it.

Code:
alias check-channels {
  var %cnt = 1
  var %ttl = $chan(0)
  var %mode-errors = 0
  var %names = %channels
  while (%cnt <= %ttl) {
    if ($findtok(%channels,$chan(%cnt),44)) {
      if ($chan($chan(%cnt)).mode == +is) {
        var %names = $remtok(%names,$chan(%cnt),1,44)
      }
      else {
        inc %mode-errors
        var %mode-problems = $iif((!%mode-problems),$chan(%cnt) $+ : $chan($chan(%cnt)).mode,%mode-problems $chr(32) $+ - $chr(32) $chan(%cnt) $+ : $chan($chan(%cnt)).mode)
        var %names = $remtok(%names,$chan(%cnt),1,44)
      }
    }
    inc %cnt
  }
  var %chan-errors = $numtok(%names,44)
  if (!%chan-errors) && (%mode-errors == 0) { echo 04 -a Check completed, no problems found! }
  elseif (%chan-errors) && (%mode-errors == 0) { echo 04 -a Check completed, no mode errors detected, but the bot is NOT present on: %names }
  elseif (%chan-errors) && (%mode-errors != 0) { echo 04 -a Check completed, %mode-errors mode error(s) detected: %mode-problems and the bot is NOT present on: %names }
  elseif (!%chan-errors) && (%mode-errors != 0) { echo 04 -a Check completed, %mode-errors mode error(s) detected: %mode-problems but at least the bot is present on all channels. }
}