Thanks for your bug report. I have not been able to reproduce this issue here so far.

Tested with a clean copy of mIRC, with the changes you mentioned in your post: confirm when pasting > 10 lines, and single line editbox. I used a small script to count the number of pastes using on INPUT:

Code
alias resetpastecount {
  %pastecount = 0
}
on *:input:*:{
  inc %pastecount 1
  echo 4 pastecount: %pastecount
}

After repeatedly pasting into different types of windows, including channels, queries, dcc chats, status, etc. the pastecount was correct for the number of times I had pressed Control+V.

Which version of mIRC and Windows are you using? Are you using any applications that modify/monitor/etc. the clipboard?