Okay, firstly one of the files that you emailed me is badly formatted. If you look at it you will see hundreds and hundreds of blank entries with no content. That threw a total wobbly when I tried to enter it. That should be producing an error message really before it tries to insert the contents into the database. I'll look into it when I have time.
The actual problem was caused by selecting the category column on the CSV file but when it encountered a row that was blank it threw an error. I've now changed the code so that if the category is empty it just passes over it and the post has no categories added to it.
I've tried it on a test domain and I created 1000 items: http://www.wordpress.andywalpole.me/
I'll email you the new plugin. If it works okay can you let me know then I'll release a new version to the WordPress depositary.