I had the same issue. 64-bit java, windows 7.
placed the advanced pipe, right clicked it, then minecraft gave me the dirt filled screen. Was then unable to access the sever.
In order to get back on, all i had to do was restart the server (I'm running it from my computer)
Afterwards i was able to remove(not right-click!) the pipe w/o any trouble.
Not gonna touch those until the next update!
Edit: actually, i'm running build 0.5.4.9. I think this might make a difference in results (not at all sure)