Issue with external drives. Some p2p sharing programs work fine with external HDD's. As you know LW never has, however I've never tried using one with LW 5. Likewise in my experience LW has problems accessing all the files at the moment it opens. Thing about external drives is they are not always 100% active, they tend to sleep a little. There can be a momentary lapse in getting the drive reading which I believe is what affects LW.

On my old computer when opening LW, LW would often even 'forget' that it was directed to share from / download to an external drive. Seemed slow in loading shares from the external drive also.

My advice to you would be to make a backup of your LW preferences, perhaps on a daily basis just before/after you quit LW for the day. Then if LW shows less shares next day, quit LW, replace the preferences folder & restart LW.

I think if LW cannot 'immediately' find a shared file, it simply removes it from its shared list. Exception might be if a user was sending a request for a shared file of yours at same time LW was opening & that might give the 'cannot find file' message.

As for copying files from computer to external for backup purposes, Firewire 800 is more than fast enough for me; more than double the speed of USB. Even Firewire 400 is faster than USB for that purpose. Windows systems might work a little better with USB than macs do, not sure. But then even my external drive listed capabilities lists FW 400 as faster than USB.

Have you considered adding a 1 TB internal HDD?