Magento Updating Stock from CSV file - custom script fix

I have a custom script which updates stock levels in Magento (multi-site installation) from a CSV file which has SKU and qty in. For some reason this is stalling with one site . So, I need a Magento/mySql/PHP guru to see why it is stalling and come up with a fix. It is hosted on a VPS cPanel server, a live site. I'll give you access to the FTP side and can also give mySql access (although I doubt you'll need it). I'd prefer not to give you Magento backend access. Thanks Jim