You'd think FTP is FTP... but I don't know if Fling is better than WL's upload or not...
You tell Fling where to upload the files, but it will upload all files in a folder to the same location. I use it to watch a folder for the appearance of a new image file (hi-res photo), then it will FTP to my website... works great for that.
I've never had an issue with WL's uploads, but it would be interesting to see what happens when you set WL to just create the files, then let Fling do the uploads...
I spent probably over an hour last night searching for programs that will selectively watch at the file level for changes, then upload--but didn't find any free programs... there didn't seem to be a lack of programs you'd have to pay for, but I didn't look into those at all...
Here's a path to go down though, and someone else might know of a program that simply monitors a file for a change status, when changed, it will execute a program of your choice--which could be a command line FTP program that will then send the file anywhere you want... but I couldn't find anything like that... at least not for free...