I have a similar experience...an elearning package of 250Mb and I have several versions of it.
The system always keeps cached 2-3 versions, but it doesn't seem to matter. Everytime a user accesses an assignment it starts loading (some times it may take up to 5').
This is because as I see, the system tries to uncompress the whole package again and again.
In moodle, the package remains cached in one single directory and it does not seem to recache everytime