Docedison:
Why not allot 3 spaces as a permanent margin?. A left justified number is certainly no less visible than any other. I would think that 999 lines of comments, fonts and/or whatever should be enough for anyone. While you're at it you might fix that behavior that causes the scroll wheel to close the boards list or any list for that matter...Doc
Drat... I thought I had the answer to do a quick pre-scan of the file being opened and allocate enough digits. But that doesn't take into account what happens when entering a line in the middle somewhere that increases the total line number quantity from 99 to 100... Maybe a re-scan and adjust if needed every time a new line is created and destroyed?
I'm not sure exactly how my favorite text editor (PSPad) does it. I just opened two randomly chosen ASCII files in PSPad, one with 11095 lines, and the other with 6 lines. In both, the background of the line-number area is light gray, and the numbers are left-justified within that area. For the file with 11095 lines, the line number area is 5 characters wide no matter where one looks at the file. The file with 6 lines has the line number area 2 characters wide. Unfortunately, while PSPad is freeware, it isn't open source so I doubt you could take a look under the hood to see how it handles changing quantity of line number digits.
BTW, I do like how in your screenshot you have lines that have nothing but comments in them the line number is colored the same as the comment. Not something that PSPad does, so that is something you are doing that is better than my favorite text editor... 
Now to install your temp files to help beta these enhancements.