Hey guys.
I had one other issue like this and i investigated it.
User`s site was using flat rate shipping. The Flat Rate shipping rate for US All 50 states was set to 0 and each products had a flat rate like 5$.
On the users website the 5$ were not being passed on to PayPal. It drove me crazy cause i just could not figure out whats causing it.
Then i downloaded his whole store and ran it on localhost. No changes, no plugins disabled and with his theme and it works just fine.
I also tested on my localhost using a fresh setup of WP and WPeC and it is working correctly.
I can only assume it has something to do with the hosting you are on.