Basically there are two sets of settings now... one set for the old bitmap font style, and then a new truetype_* set that will be used for truetype font.
The reason there are two sets is just that when you connect to USB, the /mnt/onboard on the Kobo vanishes so it may appear on the PC instead. And then MiniClock no longer has access to the fonts, so it falls back to the old bitmap font mode instead. (That and you could be deleting or renaming the font without remembering that MiniClock is still set to be using it.)
For MiniClock to show up as you like it in both reading mode, and USB connection mode, you have to configure both the way you like.
If either doesn't show up there's a configuration error, or maybe a problem with the font file. Of course it's also possible there is still a hidden bug in the miniclock. Or simply a caveat, like the clock not appearing when the offset pushes it off screen - start with lower numbers
If you post your config I can check for obvious errors.
Regarding capitalization, /mnt/onboard/ must be in lower case, everything else is case insensitve unless you're also using my ext234 mod which is, uh, hidden somewhere and I'm not even sure if it still works