it seems there is an odd line numbering bug with long, wrapped lines. the line number jumps around, line 6 becomes line 7 etc. without wordwrap its ok.
i know that it may be an edge case and one doesn't really work with such files often (if at all), nevertheless its a bug . you can test for you self with the attached php file (linebreaks, whitespace removed).
PS: regex search replace is very slow in such files, just try ; -> ;\n