It affects complex ships with inactive engines. The issue comes from calculating total thrust for the stage. When doing so, KER will calculate it using both active and inactive engines. It makes sense for future stages, cause right now the engine is not active, bus will become such when you stage. But for some ship designs it doesn't work at all. Here's an example:
I have a long rover/ship with 2 sets of engines: 1 for vertical take-off, second for horizontal propulsion. Their thrust vectors are orthogonal, some are facing up, others are forward. To switch between them I use an action group which activates/deactivates engines. There is only one and final stage in this ship.
When I take off, I don't care about nodes and burn times. But when I switch to the second set of engines and do orbiting, I need to use maneuver nodes. Usually I rely on KER's time to burn, But it is wrong because of Node Burn Time because of Thust.