usually it is the TCP connection that timesout. this can be influenced with the event 'enable workarounds'. In the settings for the event you will find the option to extend the timeout for the connection to max 999 secs (will be modified to be 9999 in 7.1.6.).
A rule should be place high in the tree and coul look like:
"If URL.HOST equals my.server.net Continue and Enable.Workaround(SetHighTimeout)"
If this doesn't help, I suggest opening a support ticket.