When reconsiling a Split Transaction in the Transaction List, if you select all items in the split and flag them as Reconsiled then the Running Total value 'ignores' the individual Split values.
Even though the Transaction List Running Total is decremented for each entry in the Split. After the last Split entry shown in the Transaction List, the Running Total goes back up to the value before the Split entries.
You have to go into the Split Transaction and flag it as Reconciled there to get the correct Running Total value.