I've also been having this issue. The game freezes up while saying "Network not Responding" every 2-5 minutes, when trying to enter any relay, and at the end of completing any mission. It's manageable, but annoying to deal with, so I've just stopped playing the game until a fix is found out.
The game was working very well for a month straight and only just started happening when Lavos came out. So It probably has to do with an influx of too many players for the servers to handle.
I've looked into every fix from forums and advice from moderators. I've done the following: