Ok, thanks for the feedback.
I'll take note of this matter and see if I can install some resource stats to see what can be happening.
We never needed before as the server always supported all the load, it's time to see where and how it is being used.
In the meanwhile, I would recommend using FileZilla as FTP client to upload files. One the best features is that it will keep a list of files that failed for some reason to be uploaded. This way you don't need to repeat the whole upload for the project but only try to upload the files that failed in the first place.