I know found a workaround and the exact problem:
1. Create two nodes.
2. Create a group for each node, including one node each.
3. Create an edge between the two nodes.
4. Then collapse (minimize) the two groups.
5. Use the hierachical autolayout function.
6. Now select the edge and use Tools->Reverse Selected Edges.
7. Use the hierachical autolayout function. The two groups will turn.
8. Now expand (maximize) the two groups. The edge takes a weird way.
9. Use the hierachical autolayout function. The two groups will turn back to the old state.
On greater files this behavior causes edges to disappear.
Workaround: Only reverse edges if all groups are expanded.