1. Yes, I switched off that dialog, of course. I couldn't find it after switching on either. But I possibly overlooked that "more".
You must enable Copy confirmation dialog first:
Preferences/Panels/Confirm drag&drop operations.
Than on "drop" you'll see a dialog, press "More" button and uncheck "Set permissions" checkbox. You'll probably want to check "Use same settings next time" too.
I think you should have this at "0" as a default. I've not seen any other product which changes existing permissions each time you overwrite a file, so doing this as default is not what people expect.
It is off by default since build #110.
I also had problems with text files always getting transferred binary, that was the other reason I switched back to WS-FTP. That option is also on this "dreaded" dialog.
"Automatic" transfer mode is turned on by default.
I suggest you add .pl and .sh files to the list, because these also need to be transferred in text mode usually.
These extensions are included since build #101. However this did not affect current installations, even if you've upgraded.
Can you tell what "PreserveReadOnly=1" is for?
This has effect on download only. I means, that if you are downloading file that you don't have rights to write to, it is marked "read-only" in local directory.
It would be nice to have a second file extension list which triggers adding the executable bit, so that f.i. .pl files get first transferred in text mode and then made executable.
Good idea, I'll consider that.
Couldn't you add a toggle button or a button which launches the "Copy confirmation" dialog (or both), so one can change this any time at will?
To the layout issues: Thanks for screenshot, etc. I'll make window bigger.