Are you talking about when you have a program open and you right click, compare to, Other file...?

It might work if you pass the command line options to the program. You can go to the "Tools/Differences" preference in PL/SQL Developer. Put in the ExamDiff program in the Executable field (Mine is at C:\Program Files (x86)\PLSQL Developer\ExamDiff\ExamDiff.exe) and put in "%1 %2 /i" without the quotes for the parameters field. The /i option ignores the case. I suspect the pro version of ExamDiff has options not available in the regular version, but here is where I found the options: http://www.prestosoft.com/ps.asp?page=htmlhelp/edp/command_line_options

That works when I tried it. If for some reason ExamDiff refuses to work, you might try WinMerge (or another program you like) in the Executable instead that will remember your preferences. Winmerge is at http://winmerge.org/ if you want to try. Just put in "%1 %2" in the parameters field if you go that route.