Hi Julie,
can you confirm which objects you are looking at when you are doing the trace? Are you always looking at the cost shown in Projects, or are you looking at Cost?
There could be a number of reasons that could be to do with unallocated costs, overhead costs that aren't initially identified as a specific Project ID in cost source, or something else.
If you cna give me a few more clues we can work out what's going on.
Michael