I'm having similar problem, when I try to access the adv. wooden pipe gui while on the server my whole game crashes. I'm running my own server and it usually gives me an error message on there, but lately it has just been saying that my connection timed out.
I'm using Windows 7 and I have java 1.7 installed. The server is version 2.1.1, and I have not made any real changes to the server options.
If it makes any difference I imported my server world from Tekkit 2.0.