I have seen reports that the boot vector does not always get properly written with ISP and that it is advisable to write it several times and verify it before exiting ISP mode.

I am not sure if you can so this with FlashMagic. There is a Status/Boot Vector option under the ISP menu where you can re-programme these but it is not clear if it clears them then programmes them or just re-programmes them. Obviously if you want to change the status or boot vector bytes you would expect it to clear them first which is not what you want.

Ian