the wording here seems to refer to the old versions. There is no longer a reference to the word "ignore" since that was confusing.  the settings are "Include all songs" and "Don't include unchecked songs"

please confirm which of the above that you are using.
thanks.

This is 6.2.1 - 5077 - Windows XP - EN - cp1252. 

I'm using a custom strings.txt file, which would explain why my option text is different. Could a different strings.txt be causing the problem? I can change back and do a rescan if you want.

ah.  thanks for explaining.  yes, the custom text might be a problem.  Earlier text was confusing, and the logic was reworked to be more clear.  

You might just have to fix your custom strings.  the text for:
SETUP_IGNOREDISABLEDITUNESTRACKS_0

is now "Don't include unchecked songs"

This is the setting to have the unchecked songs not show up.  so, if your text for "ignore" is for the _1 string, then that would explain it.

You are correct that it did change shortly before 6.2 beta :)

oh, as a suggestion: if you are using a custom strings file, try to only put the strings you want changed into it.  this helps avoid missing changes to other strings in the main file. a custom strings file doesn't need to have a copy of everything, since the main strins file is always read.

I went back to the stock strings.txt file and that fixed it- thanks for the help, and sorry to open a bug for this. Should have hit the forums first. Thanks for the strings file suggestion too, that will prevent this in the future. :)