The whole GBA code is currently a little bit buggy, so for dumping roms you propbably should stay on the last somewhat stable release V27D.
Reflashing only seems to work with 5V. Probably out of the same reason why some real carts don't work with V28 ... bad read/write timings.
I also might have broken support for the Intel flashrom I added in the last commit...
There is still a bug left when it comes to resetting the flashrom to read mode since I can't find the datasheet to look up the partition sizes. So it might be that the verifying process fails even though the flashing was successful. In this case remove the GBA repro for a few seconds then just dump the rom and compare if the write really failed.