Do you only have x5000/040 right, no second x5000/020?I don't know. For me, the copy operations are fast enough, so I haven't needed to investigate this problem yet.
At first, when a year ago I tested some of my ports under amigaos4 on x5000/040, it give fewer fps in some games in compassion with my x5000/020, with the same gfx card. Then I heard from another one something of that sort. Then, when we test some DMA routines in the gfx drivers we found that they also slowers on x5000/040. Like, on x5000/020 we have in the same driver 300 Mb/s , but on x5000/040 250 MB/s or something. Then comparing of gfxbench results, giving that VRAM=>RAM copy performance on the X5000/40 seems to be at least half that of the X5000/20. See:
http://hdrlab.org.nz/benchmark/gfxbench ... 5000-|-20/
http://hdrlab.org.nz/benchmark/gfxbench ... 5000-|-40/
So, will be very-very interesting to see if issues happen also on Linux too. And if so, it will be mean that issue or Uboot and default settings, or hardware itself.
Need to think how to check VRAM=>RAM copy performance on Linux , so we can on your and my side