@ixtab: I can confirm that trying to nest collections very easily goes boom on FW 5.4.2.
Worked once w/ a single item, then tried to nest two items at once, CM's UI went kablooey. Exit CM, the collections item counts shows 2 items instead of 3 (both in CM & the framework), but neither CM nor the Framework sees anything in it. (I have CM set to only show collections, and I was nesting collections) [EDIT: same result even without CM set to only show collections].
A flat, untouched Calibre import seems fine, though (device registered, in airplane mode, and with 0 cloud collections [0 collections, period, actually]).
As a sidenote, and this may be a Kindle issue, unrelated to CM: collections appear in the 'Active Content' filter of the Homepage?
EDIT: Actually, even when it doesn't blow up in CM, the framework doesn't seem to like nested collections (item count inaccurate, but not 0, and doesn't show any actual content when opened).
EDITē: Moving books (as well as collections) into a collection leads to the same result. Copying seems okay, since that's what the import does, and that works.
EDIT^3: Created a collection from the Kindle UI. Still appears in the 'Active Content' filter. CM doesn't see it, and 'Delete All Collections' doesn't affect it.
EDIT^4: Haven't managed to reproduce the broken CM UI thingy from my first test, though.
----
Long story short: copying works, moving (and thus nesting) doesn't

.