In reviewing a recent "Income by Customer Detail" report [our company
uses Quickbooks 2001], I noticed that although most entries under
"Type" are invoices and linke to the "Sales" account; we also have
entries where the account appears as "Cost of Goods Sold".
Additionally, each charge with related to COGS appears as a negative
entry which then causes the sales balance to decrease. Similarly, in
our COGS history some entries appear as linked to "Type" invoice and
then linked to sales account not COGS. Any explanation would be
appreciated including corrective steps that we need to change within
our accounting system.

These are not inconsistencies.  They are different types of sales.  It
seems that the invoices that are linked to the "sales" account only
maybe for services (and thus do not have any goods/inventory you are
selling that would trigger a COGS transaction).  The invoices that
produce a "COGS" entry most likely have inventory that you are selling
to that customer and, indeed, it will reduce the amount of revenue you
are making off that customer because the COGS entry is how much YOU
paid for the thing you sold to the customer.  You can view the invoice
detail to see if I'm right.

phobosca, CPA