Are you trying to upload more than 5000 rows? What is your file size?
From my recent experience in trying to import large amounts of data using Data Import Tool. It seems that 5000 rows limit is the max allowed by the tool, but it is not neccessary that all files with 5000 rows are less will get imported successfully. In fact some files with 200 rows have failed for me. What worked for me is cutting down the number of records even further by looking at the amount of progress that happens before you get the timeout error.
Though there are some posts trying to find a way around the timeout error. My guess is you can save a lot of time by manually(or writing a script) splitting your imports.
Also. Hopefully the version 10 release will save the day with its “Enhanced Data Import Tool”.