If 2 tanks connected via Attach-O-Tron from Station Science (http://forum.kerbalspaceprogram.com/threads/54774), but both tanks have direct pipe connection - pump don`t work (fuel transfer buttons disabled)

Copy-paste from the Station Science page:
"This mod also adds a new "prototype" Attach-O-Tron docking port. This port is placed early in the tech tree (same node as struts) to facilitate building space stations early on, but has several limitations. The most important is that it does not permit fuel transfer of any kind. Even manual pumping cannot pass through the Attach-O-Tron."
This is not a KAS problem in any way.