I've had the same problem for about a week now, after I started using Win7 and got SS NS 13e. Soulseek runs fine, but at times the program kind of disappears. Task Manager shows SS is running, but there's no way to access it. It doesn't matter if I send SS to taskbar or if SS runs behind other windows, it can disappear from either. I've tried ticking an un-ticking "Auto-set away when minimized" but it doesn't sort it.
you should use SoulSeekQT, because NS 13e is outdated.
Also, SS doesn't seem to "remember" anything from this kind of stealth activity. When launching SS again, I get the port conflict message, new SS starts and the old, disappeared one reappears but is disabled. Any search I did in the old SS doesn't show in the search dropdown menu.
It sounds like the client is getting sent to the hidden part of your tray:
You can also uncheck Options->UI->Minimize to tray if you wish the client to remain in the task bar.