I've been getting server timeouts when trying to connect and I've been getting kicked off the server more than usual.
Also, the only way it will update successfully is if I use Arc to launch the game. Don't ask me why, I just do. If I don't I get the message "A file is locked that can't be opened for writing." Or some such.
Wait isn't Yahoo IM part of your computer tho, so that would imply it could be your ISP experiencing issues? There is a thread in the bugs section on how to diagnose Lag etc and it would be useful if you did what it says to do because it tests your connection to STO and if your ping was high or it was being blocked at any point in the road to the server it could explain your issues.
If your connection is flaking out on it own I'd check with your ISP and get them to check your connection.