I store my PortableApps content on my thumb drive and in my Dropbox (SkyDrive's not efficient enough for this) folder. The below applies to using it with Dropbox on personal devices.
I don't have the time to thoroughly test this out, but I think I'm getting the "Did not close properly..." message upon opening Miranda IM Portable on my desktop computer, after hibernating (i.e. not allowing Miranda to set some sort of flag for proper exit) the laptop. Is this a known issue? Is there a way to circumvent this problem, other than installing a copy of Miranda on the desktop?