$chr(3) is the CTRL+K control code. mIRC is just saving the colors of the lines (which can be enabled by checking "Line colors" in the logging options window).
Notice that the ending parentheses are also not showing up in the quit messages (since there is a CTRL+O code there as well).
Naturally, since mIRC is just loading the lines back into the buffer, there are going to be issues because putting a color control code at the beginning of the line is not the same as echoing a line with a particular color. Most notably, if you used CTRL+O, the expected color would be different in each case.
However, even noticing this, it looks like what you are experiencing is in fact a bug, because I can't think of any reason why the lines with colors at the beginning would be handled differently than the ones without. In other words, why do the colored lines revert to black when CTRL+O is encountered, but the uncolored lines revert to white?