When running P4Merge, the comparison method is always initially set to 'Recognize line ending and white space differences' (aka all changes). I want to use 'Ignore line ending and white space length differences', but I have to manually re-set this every time the tool runs.
I have changed the setting:
and it never sticks. In fact, the preferences dialog entry is reset every time I go back to the menu, without even closing the program. I have changed the setting before using the Exit command from the File menu and before closing the window, and also before saving a merge.
In the past I was able to save my setting and have it be remembered, unfortunately I don't have any recollection of the software version involved. I was using P4Merge as standalone and none of the rest of the Perforce suite was installed.
I can update with any other supporting information that might prove relevant.
[Edit: It's the radio button setting in the preferences dialog that ignores changes and resets every time it's viewed, not the File submenu.]
It looks like this issue was fixed in 2013.3. I ran into this issue, updated to the latest version of P4, and the problem was resolved.