Are you talking about comments in the code, or reporter lines on the results?
I've never had any sort of problems with the code comments as you can use space or tab, but have seen where the results seem to parse out extra space. I haven't worked out any solution to the results.
The other day my wife said we were out of mustard, so I should start milking some cows. I told her that was crazy. Everyone knows mustard comes from goats!
Change the font to FixedSys and everything will be alignable and stay that way. Of course, this means you need to get everyone else to do the same so they don't screw the spacing up when they view/modify your code.