Mysql Insert/Update Problem

here is what i am trying to achieve,i have 2 servers. Win2k and linux. mysql is running on my linux server.now i have quite a lot of that i need to update on linux server from win2k machine. here is what i am trying to do.i have a PHP CLI script that will open a dbx file extract records from the dbf file one by one check is the record is already on the linux server (mysql database). if the record is already on the linux server then it will update the mysql database on the linux server. but if the record is not in the mysq database running on linux then it will insert the record. the script is running on win2k server. there are 6 dbf file that i need to extract. comcat.dbf contains 581 records comgrp.dbf contains 79 records comsub.dbf contains 1896 records manuf.dbf contains 793 records prodaux.dbf conatins 170000+ records products.dbf conatins 170000+ records the script it taking to much time while inserting. it almost 24 hours now and still it isnt finished.what can i do to update the db faster. thanx for any help in advance Haseeb Iqbal.