Here are problems I have noticed with FTP (unless noted, these are long-sntanding bugs that appeared in early 8.0 versions as well as 6.x for some (ie: file download probleme for ex.)):
Problems while downloading very small files => resulting file is 0 bytes long: this already happened with 6.x, and happens on a lot of different network & windows setups... nothing to do with server, firewall/antivirus stuff (actually I have yet to find a configuration where the problem doesn't appear).
Sometimes using "back" in FTP won't go back to the previous directory but rather will go to the root of the FTP: very annoying... (this may be due to the fact connection from the FTP has been closed though)
Sometimes DOpus won't connect to the selected FTP but to another one from the list... Re-selecting the FTP will make it connect to the other one again. This is quite rare but it already happened several times.
Regarding #1, GP Software is aware of this problem and they have been trying to reproduce the circumstances that will cause it to happen. So far they have been unsuccessful so if you can find a "happens every time" way to reproduce the zero byte download problem, please submit it. In the meantime the investigation into that mystery is ongoing.
Regarding #2. I do a lot with FTP but when I'm connected I never use the back button. Not sure why, just habit I suppose. I'll start using it now when I'm connected to my FTP sites and see if I can reproduce that problem as well.
I've been working with Greg @ GPSoft on the small files FTP problem. They still can't make it happen locally -- must be a network/latency thing -- but I've been given some debug versions which print diagnostics and I think we're getting close to understanding the problem.
I submitted that as a bug last year and it was supposed to be fixed but it still shows up. It happens if the FTP connection times out and you hit either the Up or Back (presuming your last directory was up one level) buttons.