Thanks! That was indeed the reason.
> Is there a reason for this?
Yes, there is. You must have had this TM opened at one point along with your project. Then, the project "remembers" this resource. Close that TM tab and save the project to remove the TM from project's resources.
This is what happens:
1) I finish a JP-IT project and quit CT
2) Then I open CT to do an unfinished EN-IT project (by selecting source and target language and the right file in the dashboard). From the dashboard I also uncheck the JP-IT translation memory remaining from the previous JP-IT project
3) When opening the translation file CT insists on using the same JP-IT translation memory, although it's not selected in the dashboard
Is there a reason for this?