In that case it's not a case of your connection dropping due to time on line then.
Are you using a proper FTP program or using FTP via window explorer? It can do randomly silly stuff that way so if you haven't got one already a dedicated FTP program is the way forward. I use flashFXP and it's brilliant. You can download a 30 day trial copy from
www.flashfxp.com then if you want to continue using it you can do but you need to purchase a licence. It's not expensive though, something like $25 or there abouts.