Thanks for your help. Yes, the custom names appear in the file you edited appear but I think you were unable to replicate the bug because you created new transformations rather than editing existing transformations from a file.
In the attached image, you will see that I edited the chemistry and the name of your first transformation. The chemistry change persists in the exported file (also attached) but not the name change. However, the new transformation I created persisted with it's custom name. It's a pretty subtle bug but I think you will be able to replicate it if you edit the attached configuration file.