Hi,
I am not sure if I get your question correctly.
When creating a J-Flash project, it is user's responsibility to perform the correct EBI setup with correct timings.
It is a bit weird that if you are skipping the first 2 sectors
everything always works correctly...
Maybe there is a problem with the nWP pin?
After having a look into the flash manual I found the following:
The Write Protect function provides a hardware method of protecting the two outermost boot
blocks. When VPP/Write Protect is Low, VIL, the memory protects the two outermost boot
blocks; Program and Erase operations in these blocks are ignored while VPP/Write Protect
is Low, even when RP is at VID.
It is not totally clear to me which blocks they are referring to (the 2 first ones, the two last ones or the first + the last blocks),
but if they are referring to the first 2 blocks it could be an explanation for the problems you are seeing.
Best regards
Alex