Backing up to two external hard drives

I have two external hard drives - a LaCie FireWire (my first purchase) and a small Targus USB (used while travelling). Backup software is Silverkeeper. I used the LaCie exclusively for about six months with no problems. The initial backup was lengthy but subsequent backups were much quicker, since it was merely an updating process.
The LaCie stayed at home and the Targus was used for four months. It performed in exactly the same manner.....lengthy on initial backup but quicker on subsequent backups.
What happens now is that every time I try to do a backup, alternating between the two hard drives, the software indicates that no backup has ever been performed and I must start from "scratch". In addition, I get a window telling me that if I want to create a bootable back-up, the destination volume must be totally blank. (I do realize that only the FireWire drive can be a bootable copy).
I am totally baffled. Any suggestions?

Sue
Whilst I totally recommend SuperDuper!, and use it myself, be aware that the more advanced features like the fast Smart Backups and scheduling are only available from the full (registered version). The free version will only do a full and complete clone.
That said I think SD! is well worth the asking price and definitely my primary choice.
15" 1.25GHz/12" 1GHz PBs, 2xPPC Mac minis, 12" iBook G4,   Mac OS X (10.4.6)   Cube, 2xTAMs, iPods 2G/4G, iPs, AEBS, AX

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