Can't join two lines at single node

AFAIK you can only join end-nodes together.

Make two lines, select both, combine (ctrl+k), use path tool to select two of the end-nodes, click "join nodes", voila. Works for me, but like I said only with end-nodes.

Is that the problem?

I think pbhj is correct - although the Combine Nodes tool is selectable, it cannot be used to combine two nodes unless they are both ends of paths. When you create a path with the Bezier tool, if you click very near the first node it thinks you're trying to create a closed path and closes it for you. You can later cut the path at any of its nodes by selecting the node and using the Break Path At Selected Nodes tool. Also, you can cut a path by removing one Bezier with the Delete Segment tool. You don't need to know which was the original end node.

With any two end nodes, whether on the ends of the same subpath, on two subpaths of a combined path, or two different paths, you can select both with a drag or shift-click, then there are two tools to Join them, either by adding a new segment or merging them physically.

The nodes and control points of a closed path have an order, which is used when, for instance, combining subpaths into an object such as the letter 'B'. If you break and recombine bits of paths, I don't know if you can be sure which order the nodes will go in, nor which will be listed first in the XML. Order can be reversed, as is needed to ensure the holes in the letter 'B' are treated as hollow.
When you join two different paths Inkscape somehow decides which one gets to propagate its genes, i.e. fill, stroke and so on. I can't work out how it decides this. It isn't Z-order.

Hope this helps
Chris