Android Recovery is a linux box - it is quite capable of correctly partitioning your SD card.

(but recovery scripts don't always give you the widest variety of options, depends on the recovery of/c)
I'm going to guess that the real problem came up the next time you inserted that card back into your windows PC - suddenly windows can't read it! not even the main partition that most guides claim should work fine! ... well how odd, but windows offers to format it for you, and then you restore your backed up SD card data, because you were clever and made a backup...
I ran into a scenario where someone did exactly what I described above, and (on his laptop internal SD card reader at least) after windows mangled the card during formatting, even MiniTool was unable to recover the lost space.
(though it was restored after a full wipe)
Moral of the story: internal SD card readers + windows =
Also, sorry if i made the situation sound more dire than it is - if MiniTool can't see the second partition, just make a backup (copy, zip, rar, or some fancy backup tool as desired...), full wipe, restore backup
