Inventory Close runs very slowly

I know that negative inventory can cause the inventory close to run slowly, so that is 1 of our issues, but we are also configured with 2 sites and have BOMs that have lower level BOMs that exist only in the other site.  Dynamics does not cross sites for BOM costing, does it also have a problem being able to settle transactions for items on a BOM that exist only in the 2nd site?

Thanks!

Melissa Ingram