Keiko Dalton

I'm not sure if I remember it correctly, but I think that alignment uses settings of a project which is selected in the projects list in the moment you start the alignment (weird, unexpected and undocumented behavior, yes!).

So you should either make sure that the "Process unsupported versions" option is turned on in the project settings of a project you have selected before launching the alignment, or check the Settings accessible from the actual alignment process/dialog.

Hi Keiko Dalton 

Unknown said:

I understand that before you want to process the newest version of InDesign CC files in a project, you would need to check the box for "Process unsupported versions".

However, in my case, I'm just trying to create a TM from a pair of files.

It makes no difference what you are trying to do.  For Studio to be able to parse the files the settings need to be appropriate for the files you are trying to open.  Have you tried this option?