Please take a look at the following solution
https://oss.azurewebsites.net/forum/flashf...html#post82582
Check your FlashFXP settings for the TCP/IP keep alives,
* if they're off then turn it on.
* if its on and the interval is 20 minutes or less increase the value or turn it off.
* if the value is greater than 30min try to reduce it to 15min.
After making this change try to upload the file again and see if the timeouts continue.