what are the windows and mac equivalents?
I suspect that JungleDisk is primarily to blame here. Most programs (certainly the Windows search indexer) already know to treat files on network drives differently, otherwise they'd be unusable in business environments where you have a variety of SMB shares mounted on every computer.
If JungleDisk appears as a local drive, there's your problem. This is just speculation though, as I can't be bothered to give them my credit card details just to test that theory.