I experienced this problem 3 x within Transit packages. Each package included about 12-15 files, all completely translated except 1 file.
Shortly after we decovered the reason: the name/designation of the respective files showed some special German characters: ä, ü and ß. Since the TM saved all data, we renamed the files and translated them again.
Everything worked smoothly!
So check your file´s name and maybe you will find the motive...
I renamed, pre-translated and exported the original package and it worked
Thank you very much!