Let me see if I can try to clarify what's going on.
You generate a world. I'll use Region5 as the world, just because that's what you seem to currently be using. You have seasonal autosave and backup option turned on.
Save Folder contents: Region5.
You create a new fortress. The game does a seasonal autosave and back.
Save Folder contents: Region5, Region5-spr-301.
You play for a while, then save and exit while still in spring.
Save Folder contents: Region5 (this has your current data), Region5-spr-301 (this is your fort at the moment of embarkation).
You resume playing, by selecting the Region5 folder. You play through summer.
Save Folder contents: Region5 (this has your summer start data, until you actually save and exit. If you crash out now, this folder has your summer data), Region5-spr-301, Region5-sum-301 (summer start data)
Now, if you continue opening Region5 every time, Region5 will always have your most current data. But given your directory, at some point, you opened Region5-spr-301. At that point, the game does not treat it as being a seasonal save of Region5. It is a save of "Region5-spr-301", a different region/world/timeline as far as the game is concerned. When you got to summer, it autosaved. The autosave is always created by appending the season and year to the current save folder name, within a character limit. This is why if you play Region5 continually, you end up with Region5-sum-301, but if you loaded Region5-spr-301 and go to summer, you end up with region5-spr-301-sum-301. Then at some point you loaded region5-spr-301-sum-301, and played to autumn, at which point it tried to append aut-301, but the string was too long, so it truncated the original name first, down to region5-spr-301-sum-, and then appended -aut-301, so you ended up with region5-spr-301-sum-301--aut-301.
As for your last post: You seem to be mixing up autosave and backup options. The autosave option saves your progress to your current folder at certain intervals. The autobackup option makes a second copy of that save, with a different name (the current folder name with season and year appended). Neither option change which folder your progress gets written out to: it's always the same folder that you loaded your current session from. I'm not sure how that isn't clear from the text for that init option, or how (or even what) you would expect it to behave differently.
And you couldn't have ever noticed the behavior until you turned on backups because it never happens otherwise.