Sorry, I was talking nonsense. This is the correct reason why:

Code:
on 1:TEXT:*:*: {
  set %capscheck $remove($1-,$chr(32))
  set %capscheck1 $strip(%capscheck)
  if ($caps(%capscheck1) >= 50) { 
    msg $chan 04 $+ $nick 02you are using 04 $+ $caps([color:red]%capscheck1[/color]) $+ % Caps. 02this is 04VERY 02annoying 
  }
}

Before you used $1- where the red is, that still has the spaces in.

Code:
on 1:TEXT:*:*: {
  set %capscheck $remove($1-,$chr(32))
  set %capscheck1 $strip(%capscheck)
  if ($caps(%capscheck1) >= 50) { 
    msg $chan 04 $+ $nick 02you are using 04 $+ $ifmatch $+ % Caps. 02this is 04VERY 02annoying 
  }
}

Would be faster.

/me remembers to test his code frown