Are you running Windows 7 and are your mapped shortcuts stored on your desktop?
Windows 7 has a limitation of four active shortcuts (on the desktop) for mapped network drives. If Windows detects that one of the network resources is unavailable (e.g. from hibernation), then all of the networked shortcuts are deleted. This was driving me a bit crazy until I discovered the root cause.
You can map any number of network drives, but you must limit the number of networked-shortcuts to four or less, then this issue should stop recurring (even when a drive hibernates).