When uploading large files (65mb) the transfer just stops after a few megabytes and then the server times out and disconnects the connection. All other causes having been eliminated it appears there is some kind of flow control problem that causes the upload to stop - the server connection is not lost.
The size of the Transmit Buffer in CuteFTP (used to buffer uploads) just needs reducing. The new tweak option is in the config menus - go to Tools->Global Options->Transfer The Buffer settings are at the bottom of the Transfer panel - values should be multiples of 1024 bytes.
The default for both the Transmit & Receive buffers is 65536 bytes (64kb) which is fine for most servers but not all. Reduce the Transmit Buffer size until the problem disappears - if downloads are ok leave the Receive buffer at 64kb.
Recommended settings are 32kb - 32768 bytes // 16kb - 16384 bytes // 8kb - 8192kb Geeks may then wish to increase buffer size in 1024 byte jumps to find a maximum stable setting. 16kb appears to have no impact on upload speeds.
CuteFTP sets its Transmit & Receive buffers at the maximum allowed setting of 64kb - which is apparently much larger than the default for most other FTP clients. Smart FTP has the same tweak option - but uses default values of only 2kb Transmit and 8kb Receive.
Note: You must be using CuteFTP v7.0 or newer - older versions do not support the new setting.