I looked into your problem with the interlinear. There actually isn’t a bug in the Interlinear causing this. The problem is with the BTA project.
The problem is that the English language definition used by the BTA project got messed up and the character settings are not English settings (I’m not sure where they came from). They also define the lowercase characters as uppercase and vice versa. Because the language settings are shared between projects, this caused the settings for other English projects to also be messed up.
Fixing the characters in the English language definition (Project > Language Settings > Alphabetic Characters tab) fixed the interlinear issue.
Note that you may have to restart Paratext to see the fixed settings.