Add "ignore inconsistent line endings" project option
We have a lot of data in character-based columns that is essentially the same, but because of inconsistent line endings (CR vs CR+LF) cannot be easily confirmed as "identical". For each cell we have to open the viewer and visually inspect whether we only have line ending differences or there are other (meaningful) differences.
If you're comparing procs you might be using SQL Compare instead of SQL Data Compare - we do have an 'ignore whitespace' option in SQL Compare which will mean that different line endings are treated as being the same
The tool is pointless for comparing procs, it says all proc are different because of line endings!