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I noticed that running Executive with default settings at the same time as running an ftp client seemed to make the transfers more stable. I don't know why this would be the case, or if it was even just chance. Executive is an alternative multitasking algorithm.
Like someone else said I also transferred to or from ram wherever possible.
I hesitate to suggest this as it was a few years ago, but you could give it a try since Executive is freely available on aminet.
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