Hi,
is it possible to add an option to "cache" the opened ftp connection for x minutes?
in this manner the upload speed is better (now it seeme caching for a very short time the ftp connection)

You could send a keep alive every x seconds

keep-alive commands are sent to all opened FTP connections each 30 seconds.
If phped does not do it, please let me know md5sum of phped.exe.

where can I find md5sum of phped.exe? I dont'run linux

I think it doesn't send the keep-alive (or the ftp server ignore it) because if I do several upload with small pauses between them, they are very fast at starting. If i just wait 2 minutes I've to wait some more seconds for the startup of the new connection

http://forum.nusphere.com/sshot/md5sum.exe
feel free to use it, it's free

regarding FTP, check if server session timeout is more than 60seconds.
Also, you may want to enable logs to see if PhpED issues nops, pwd, cd ., and rest 0 each 30 seconds.