Start a new project, looks like Tunerstudio somehow corrupted your old one.

I got similar on my netbook. This is what I did:

1) Renamed project to Old_Miata
2) Copied it as Miata (previous project)
3) Renamed last uncorrupted msq as "CurrentTune.msq"
4) Connected to MS and kept the Controller tune.
5) Saved the tune.

This allowed me to keep all my old, uncorrupted, saved tunes, as well as logs.

Once all was well, I deleted "Old_Miata" project.