Another thing just happened.
I'd forgotten to save the password to the ftp server so when I left alone it bombed out and sat there asking for a password. So I entered it and lo-and-behold it resumed.
However, I amended the password in Site Manager whilst it was downloading, assuming that it would not take effect until I reconnected properly, and again it failed and was waiting on a password.
This time I came out of FlashFXP, went back in and reloaded the queue. it automatically logged in
but didn't resume again