So far as I understand, there are 5 possible reasons:
1.) LoopTool's Circle menu settings may be the culprit:
The settings used restrict it's alignment. Try other combinations.
2.) Duplicate vertexes and/or lines. LoopTool's tools depend on nearest-neighbor objects. This may indicate that the mesh needs cleaning.
3.) Multiple plugins may cause undesirable operation. Try removing other enabled plugins and try again.
4.) Possible driver conflict. Verify that the drivers your system is using is compatible and up-to-date. You might also need to use an older version of a compatible driver for stable operation.
5.) Faulty Blender - A fresh installation of Blender may be needed. Also verify the storage device you load it from is in good condition, and is properly connected.