Hmm, not sure what's going on there; my Dropbox folder (which appears to be the main offender for people with this problem) is several folders deep on my second drive, since I basically have a parallel folder structure for the things that I've moved there (i.e - /Users/haravikk/Documents/Dropbox).A put the folder inside another ( folder A, in HardDrive2/folder B ) and put folder A in the Sidebar's favourite.. and so far.. after rebooting... no HardDrive2 in the favourites!
Out of interest, those who are having trouble with Dropbox, and those that are not; are you using the default dropbox folder, or have you moved it onto the other drive using Dropbox's feature to do-so? In my case mine is both in a non-standard location, but I've also sym-linked ~/Documents to be in a different location