I think that when I run my reports, it is listed on separate lines.  I'll run it with project ID as report column and they do show separately.  Could it be a report setting?

I agree this is needed.  I work for a community foundation so we use project IDs on every transaction.  Having to work around this issue is time consuming.  For example, I ran a pivot table of expenses by project ID and could not find a way to make the distributions reflect correctly.  I even worked with a customer support associate who said it wasn't possible. I ended up having to manually key information.

Specifically which report are you trying to run?  If it is a General Ledger report, that report, by definition, is by account number, not project ID.  It may be the type and there may be a different one that will give you what you are looking for.