There is nothing to fix in my EPUBs (at least those I tried). They are hand-crafted by me, from w3c.org-validated HTML files. All the paragraphs have zero margins, there are no widows, orphans and such.

And, it wouldn't be worth the hassle for me, anyway. I buy e-reader devices for reading books on them, not to struggle with manually fixing the book files
before reading them.
I have no idea what 2.4, 2.5.2, etc., are. If you mean some internal Kobo Mini software, I have no clue -- after bringing Kobo Mini home from the store yesterday, unpacking it & running it for the first time, it offered to update its internal software via WiFi, which is what I did. I never connected it to my computer via the USB cable, because it just wasn't necessary (and that's great!). I side-loaded my EPUBs by downloading them from my SugarSync account, as mentioned. I could access the Dropbox (etc.) website in the same way directly on Kobo Mini. I love that feature!
This, I mean the inefficient use of screen real-estate, is obviously a well-known bug of Kobo readers. I had known about it
before buying Kobo Mini, because I had read quite a few expert/lengthy reviews complaining about this particular flaw. Even so, the benefits of the delightful form factor outweigh the nuisance that is that huge, empty (and even inconstant in height) bottom margin, so I went ahead and bought Kobo Mini. By the way, one customization feature I'm missing on Kobo Mini is the ability to adjust
paragraph spacing in addition to
line spacing.
In a primary e-reader of mine, a flaw like this (huge, empty botom margins) would be unacceptable, but because I'll only be using Kobo Mini occasionally (for long-distance travel, when running out of iPad/iPhone juice will be a constant threat), I can live with the flaw. Most of all, it's a
software flaw on the part of Kobo Mini, so I hope it can perhaps be rectified in future by the makers of Kobo Mini, without me having to buy a new device to see the improvement.