everytime you run the game, it stores temporary files in the X, Y, and Z drives because 64MB of ram fills up too quickly.
When you run the same game twice in a row, sometimes the xbox re-uses the files in its X,Y,and Z drives instead of re-loading them, hence your faster loading time.
the problem with modding is, if the files you mod, are different that the files in the X, Y, Z, drives, the game will crash.
but if you delete these files, the game will have to reload the fresh modded files.
The game caches the gta3.img file and a few others i think.
any mods that involve these files need the cache cleared everytime you make a change.