It seems that SOPC Builder isn't able to map the peripherals in your system when forcing the bridges to address 0 to prevent an address shift. It is strange, in my experience this always worked...
I tried a different strategy. I unlocked all the bridge addresses, and saw after the base address assignment that there are two block that use two addresses: ddr2_bot and descriptor_memory.
I collapse all the components (View menu) to have a better overview. Upon a first look I saw that you had some pipelines that weren't very useful. If you use a clock crossing bridge you don't really need to combine it with a pipeline bridge. So I removed pb_dma_to_ddr2, pb_cpu_to_io and pb_cpu_to_flash. Then I reran an assign base address.
Then I right click on ddr2_bot, go to connections > s1 and see that it is connected to pb_cpu_to_ddr2_bot and ccb_dma_to_ddr2. Since locking those two bridges to 0 didn't work I tried to do the contrary. I locked the pipeline bridge from the cpu to its current address (0x08000000) and modified and locked the address on the other pipeline bridge to match. Then I did the same thing with the descriptor memory. I locked the ccb_cpu_to_io address to 0x10000000 and modified and locked the pb_dma_to_descriptor_ram to the same address.