I have reproduced similar behavior, with some big websites. Generally, the operation takes some time, because it gets your db as well. If there are any external files - not from Sitefinity, not createdby Sitefinity API they could alse be a factor for the delay. Generally, when you open the zip archive or perform some operations over it, this could corrupt it. The archive is being generated and accessing it you use it - Sitefinity could "get" that the file is used by another program.
However, if you experience such problems, there is a fast way - ftp the site to the another server and install it there.
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