This happens, when you connect a component once through a bridge and once around it.
The bridge adds an offset to the address space, so that it's cleanly separated.
So the component is seen by some periphereals at it's real address and once via the bridges offset.
I usually circumvent this by adding a second bridge into the "direct" connection, and giving that the same base address (thus adding the same offset).
You can check this easily via the "Address map" button below the SOPC scheme. It will show you which Avalon master sees which avalon slave at which address space.
The NIOS EDS can not handle multiple addresses for the same Avalon slave interface, so the should match for all masters that need to address one slave.