Large AR file update - how long should it take?

We have a client that has two companies that use VI to import AR invoices.  The import file normally contains over 4000 records.  In the first company they import the file and update the Sales Journal.  This process will take about 10 to 15 minutes.  In the other company the same process can take up to 4 hours.  It imports fine, but the Sales Journal takes forever.  They use the same VI job for both companies.  I'm thinking they may have data corruption in the files for the second company...any other thoughts on this?  They are running Sage 100 Advanced.

Sue