When you say it's skipping lines, what do you exactly mean? Empty lines? $strip could cause a situation to occur where you'd end up with an empty line. As an example: line that only has control codes in it.
Other than that, I see no reason why it would "skip" any lines, unless it's a bug in mIRC.
Here's an alternative, that will work quite a bit faster when copying large buffers:
alias chancopy clipboard | filter -wk $active chancopyx
alias -l chancopyx clipboard -an $strip($1)
