Unexpected Cash Flow report behavior. Help?

[...]

We are a private school.  Our CPA suggested we keep track of our tuition
assistance as an expense.  That is, although some families pay less, they
do so because they have been allocated some amount of the tuition we are
willing to forgo.

As an example, start with a brand new account.  Put in only one transaction:

Income:Tuition                       10,000
Assets:Checking Account        5,000
Expenses:Tuition Assistance    5,000

As far as cash goes, there is only $5,000.  Technically, the client owed
$10,000, but we forgive $5,000 of it and keep track of it as an expense.
I'd expect the cash flow report to look like this:

Cash Flow - 01/01/2013 to 12/31/2013
Selected Accounts
Assets
      * Assets:checking account
      * Imbalance-USD

--------------

Money into selected accounts comes from
    Income:tuition                 $5,000.00

    Money In                       $5,000.00

----------------

Money out of selected accounts goes to
    Expenses:tuition assistance    $0.00

    Money Out                      $0.00

----------------

    Difference                     $5,000.00

But instead, it looks like this:


Cash Flow - 01/01/2013 to 12/31/2013
Selected Accounts
Assets
      * Assets:checking account
      * Imbalance-USD

--------------

Money into selected accounts comes from
    Income:tuition                 $10,000.00

    Money In                       $10,000.00

----------------

Money out of selected accounts goes to
    Expenses:tuition assistance    $5,000.00

    Money Out                      $5,000.00

----------------

    Difference                     $5,000.00

This looks to me like $5,000 came out of the checking account, when really
there is no such transaction.  The real reason this bugs me is because
sometimes we forgive all tuition for an individual.  Then, the transaction
for the person does not have anything going into the checking account and
so is not included in the Asset Cash Flow report.

Finally, often there are transactions that accidentally have a meaningless
zero in, zero out, imbalance "transaction".  Then these transactions show
up in a Cash Flow report for the imbalance account.  So, if there was
accidentally a zero in, zero out, meaningless transaction associated with
the checking account, it would show up as cash flow going through the
checking account!

I am not an accountant.  I don't know what an accountant is expecting to
see.  But I feel like this behavior potentially makes the cash flow report
meaningless.  If this is expected behavior, there should at least be a
function that removes all of the zero in, zero out splits.

Will our accountant be confused by GNUcash's Cash Flow report working like
this?

Thanks,
  Elliot