This has been in ZQuest forever.
Simply, whatever locations Link's sprites are set to now are retained when importing a graphics pack. So, one has to manually redo Link's sprites.
(Also, on a related note, subscreens are not saved in Graphics Packs either)
SUbscreens are exported seperately from graphics packs I believe. There should be an option to do so, if not in the file menu then in the subscreen dialog.
As for the other problem, do item, enemy, etc tile locations get saved with graphics packs? Cause I'm not sure whether this qualifies as a bug or not.
A graphic pack should, in theory, store all graphical elements, including tiles, combos, palettes, and everything that depends on them, such as sprites and sub screens. I will do more testing to see what things are and are not saved.
Again, not really a bug I think. GP just aren't supposed to store that type of info it looks like.
Yes, this is definitely a bug. Link's sprites should be saved with a graphics pack, there's no doubt. Link's sprites are purely graphical in nature, and is tied to the rest of the data in the ZGP. This is obvious when you try to use it, and have to re-do all of Link's sprites.
HOWEVER.
Do I care anymore if this bug is fixed? Nope.
ZGPs are flawed because they CAN'T include all graphical data, since a lot of it (all the OTHER sprite data) is highly variable between quests. Back in the old days when the enemy, weapon and item lists were hard-coded, then you could be sure that Item 0 was a single Rupee, etc. These days, that assumption is incorrect, because I can change everything around as I please, and all the other data is not suitable for the ZGP.
Besides, the only time one would want to use a ZGP is when one is starting a new quest, and at that point they may as well just use a blank QST and call it a day.