I am having a problem with a large Delphi codebase where I work where as a side effect of porting from Delphi 2007 to XE2, we now encounter the following strange, related issues
I've seen things like this before, and IME it's generally due to an compiler bug in counting line numbers. If you have nonstandard line breaks (not CRLF) at some points--which can happen--the IDE will do proper line breaks but the compiler doesn't count them as new lines, so everything afterwards gets thrown off by one.
What I do when I encounter a file like this is open it in EditPad, convert all linebreaks to some other style (Unix or Mac style) and then convert all linebreaks to Windows style and save it. This ensures that every line in the file ends with CRLF, and after a rebuild the issue with the blue dots not lining up right goes away.