I would start by checking your firewall settings, as generally when it is being disconnected by more than one software package it is the firewall or connectivity settings within your IT department that have caused the connections to be dropped.
Next I would check that you have the timeout settings set to a high enough time frame to allow some dead time before disconnecting. The default setting on Filezilla is 10 seconds. I would recommend setting that to a higher time setting to insure that any dead time on your system doesn't cause the connection to terminate prematurely in the instance say where there is priority activity on the system and your network connection is delayed.
I would start with these two places and maybe even look into changing the port that ALM connects over (the default is generally 21, but any available port could be used upon approval from your IT administrators.
I hope this helps some,