I know I'm replying to this very late but I was having this same issue. And after hours scouring the internet and on the phone with Quickbooks trying to resolve it, my accountant was able to tell me the problem after looking at it for less than 2 minutes. It's an accounting issue, not a software problem. 

The costs that were not showing on the project overview were all inventory expenses for me. Because they were current inventory items, they were on my balance sheet, not my profit / loss sheet. They don't show as actual costs of the project until they are moved off your balance sheet and onto your profit loss sheet. Once your project is finished, you can do a journal entry to move them from your balance sheet to your Costs of Good Sold. Once that's done, you'll see them all show up. Kind of annoying as you don't get real time numbers, but that was the issue for me.