Wierd indeed...
The only thing i can think of is Texture Cacheing must be on (in fact, i bet ya a dollar i'm right
)
If you load up EQEmu and play in a zone (lets say west freeport), you get a wfreport.txc (or something like that). I'm not exactly sure HOW these files are generated but thay are (possibly with some imput from the servers)...
Now if you go into EQLive and try to zone into west freeport, its not gonna try to load the zone files, its going to load up the wfreport.txc that the client made while on EQEmu servers, which it may not like.
If this is the case, delete all *.txc and *.tmp files in your EQ folder and then turn OFF Texture Cacheing.
Other than that, EQEmu doesnt alter EQ (but sometimes the client makes files while you play on EQEmu, such as character hotkey files, txc file, tmp files, a couple ini files, ect).