Sometimes, 8-bit (256 color) tiles look fine in ZQuest, their colors are right. In ZC, they are not however. I will get a screenshot shortly. This is in 572.
EDIT:
ZQuest shot: 
Note the rupee at the near-bottom left
ZC Shot:
What happened to my rupee!
Does it use any colors from csets 2,3,4,or 9?
If so, and those change then the rupee will change. 😉
I've made it a habit to not use those CSets (but will double-check).
Also, I was editing said rupee in that same palette... so why would it look different?
Checked, and no, it is not a CSet problem, as the discolored sections of the rupee were both changed to pink and purple, but remained the color that they are in the Screenshot.
Because in ZC the palette changes in ways that aren't duplicated in ZQuest, such as CSet 6 changing depending on Link's ring.
Huh... I guess that WAS the problem... I used a CSet that made the rupee look normal, but changed for some reason in ZC. Not a bug... merely a limitation.
Been there done that. 😉