If you are using Sort by Collections on the Kindle then they are sorting by most recently accessed. Using Sort by Title will sort them alphabetically but include collections and books in the same list. One trick people use is to put a character/prefix (such as "_") at the start of collection names to force them to sort to the top.
If you're downloading Calibre you might want to consider installing the plugin in my signature to help manage your collections. Since you've already installed a hack, I think installing calibre should easy enough if you aren't already using it.
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