I believe this is a user behavior error. I would follow with the user on a step by step basis to ensure that the steps are applied as follows;
1- Cards > Inventory > Quantities Site
2- Choosing an Item Number
3- Click on Site-id radio button, and then choose a site from the lookup
4- Click Save.
If that's not working, any error message would help you out. Otherwise, you may want to dig deeper on the SQL Profiler level to check what processes are being run, and what's going wrong with the save.
One more thing to consider, item-site master table is (IV00102)
Hope this helps,