File | Save
This option simply saves the data in the grid as a Markbook90 file using the current filename. If you have created and saved, or opened a file, then the data displayed belongs to that file, whose name is the current filename. Clicking on File | Save simply overwrites the existing file with the (presumably) updated data.
In this case, you are not asked for a file name, but you are told that the file has been saved. Before saving, as a backup, Markbook90 copies the existing file to one of the same name, but extension .bak (overwriting any previously existing .bak file). This means that at any time after a couple of saves, you will have the latest version (with your own, .mbk, or no extension) plus the previous version (with the extension .bak).