Perhaps your issue is different. But when that happens to me (and it only happens when I'm designing my own templates), here's an example of what's going on:
A dimension is set to A0. It has two slots: A0 and B0.
Somewhere else, there's another dimension that starts at C0. It has 10 slots, chromatically ascending. Everything plays fine...
Until I hit keyswitch A0. This is because the tenth slot in the second dimension (starting at C0) shares A0 with the first dimension (starting at A0). And these may be completely unrelated dimensions.
The duplicate assignments are harder to find than my simplistic example. But as you can see, it has nothing to do with Groups or their naming. It's simply one instance with a duplicate assignment hiding deep in the weeds of two (or more) slots. And they often are found in unrelated slots -- not parent/child slots.
When these are triggered, the slot tree orientation may change, and it's befuddling.
Understandably, starting fresh remedies this, as does using the VSL Presets, as the former is built from scratch without duplicate assignments and the latter is assembled by our wiser counterparts at VSL.