For some strange reason FileZilla FTP client (version 188.8.131.52) kept producing timeout errors when trying to process multiple simultaneous file uploads. I was able to reproduce this behavior on Windows 7 Pro 64bit and Ubuntu Linux 11.04 64bit using the same version of FileZilla.
By default, FileZilla sets a maximum of 2 concurrent uploads. In my case, a quick fix was to simply set this value to 1, which directs FileZilla to upload files sequentially rather than simultaneously.
At this point I am not sure what causes this timeout problem, since it only occurs with one specific FTP server. Strange side fact: Other users are not reporting any symptoms of this kind on this server.
Anyhow, settings the max. concurrent upload count to 1 fixed the problem – for now.