I have discovered that loading tg3 files created by TexGen versions prior to 3.1.0 causes TexGen 3.1.0 to crash. This is due to a change in the way cross-sections are stored internally. This bug has been fixed and will be corrected in the next version. But for the time being avoid saving and loading files across versions. Note that any python scripts written for a previous version of TexGen should still work in the new version.
The version with which the tg3 file was created with can be seen by opening up the file in a text editor and looking for the second line of the file: