FWIW I've also had problems with the SkyDrive folders on my SP2.
My cloud folders (set to be available offline) include Documents, Pictures, Music, Videos, Downloads, etc, which I added to the corresponding Libraries in Windows Explorer. For example the Documents Library lists the SkyDrive Documents folder first (and as the default save/public save location), then the local Documents folder in second place.
I also enabled HomeGroup sharing, though it only seems to apply to local folders and not the SkyDrive folders (can anyone confirm)?
Now, here's what I think caused my SkyDrive syncing problems (YMMV)... By default all my profile subfolders are supposed to inherit permissions from the parent (C:\Users\[profile]) which grant full control to: SYSTEM, Administrators group, and my own account.
But from time to time, my SkyDrive Documents folder somehow got modified to disable permission inheritance, and instead had 3 new permissions added which if I remember correctly were: Administrators group, my own account, and the HomeUsers group. It didn't make sense to me since, even with the HomeUsers permission added, HomeGroup sharing does not seem to see SkyDrive folders at all. More importantly, I think the missing SYSTEM permission was causing SkyDrive to get stuck all the time.
What's strange is that none of my other SkyDrive folders ever got changed like this, only Documents. And whenever it happened, I noticed that my Documents Library also got changed so that the SkyDrive Documents folder got moved to second place, and the local Documents folder got set to be the default public save location.
More importantly, file/folder changes would get stuck syncing. And half the time when I booted up, the SkyDrive folder tree would be missing on the left-hand pane of Windows Explorer. And now that the latest Windows 8.1 update has added a SkyDrive icon on the system tray, I could see that it would get stuck on syncing status, or it would say everything's updated when it actually wasn't.
Sometimes I was able to make piecemeal progress by manually removing and re-adding files that were stuck, or renaming folders to get their status updated. By mainly, resetting the SkyDrive Documents folder back to the inherited permissions was what got SkyDrive back to normal behavior.
I'm not sure what caused the permission change in the first place. It could be something to do with some software installations, since it had occurred more often in the beginning when I was setting up the SP2. It had seemed to stabilize for awhile, until I had to factory reset my SP2 and started with software installs again...