Have you got any Disk Utilities (aside from the ones that are provided by OS X) like Norton or Disk Warrior?
If you do, run some scans to see if your HD has problems.
Next, try setting up a new Saving directory by going to Limewire, Preferences and Saving.
After doing that, click Apply and try dlding something small and popular (so that you get it fast) so that you can check if it goes in the new directory or not.

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iMac G4 OSX 10.3.9
RAM 256MB
LW 4.10.5 Basic
ADSL anything from 3 to 8Mbps/around 1024kbps

"Raise your can of Beer on high
And seal your fate forever
Our best years have passed us by
The Golden Age Of Leather"
-Blue Öyster Cult-