(1) So can I assume you use EXT mode and do not use the "PC relative"?
EXT mode: JSR $F684 ; absolute is absolute
PCREL: JSR $F684,PC ; would not work if code is relocated
Note that by relocated I mean code moved without re-assembling at new location. So which way are you relocating it? If not the problem, I can't think of anything else yet. Check for other errors... trace it.
(2) It seems conflicting only when missing something:
Vdd and Vpp should be nearly equal __for normal operation__.
Vpp must be within tolerance of 12V __for programming Flash__.