Process Payment and Split Transaction Question

[Fred Dirkse - Big Easy Cafe and Coffeehouse]

Greetings - 
I am needing some advice on how to properly pay an invoice.  
I am currently setting up my GnuCash system and am entering several
months of past invoices.  For one of my vendors, I have entered all of
their invoices (about 10).  When I attempt to record a payment of an
invoice, it is entering unexplainable split transactions in my accounts
receiveable more times than not, and not marking the invoice I am
attempting to pay as Paid.  Here is my process:

1. Business -> Vendors -> Find Vendor
2. I search for and find my vendor, highlight them, and click on
Vendor's Bills.
3. I now see my invoices for this vendor.  I highlight the one I want to
pay and click Process Payment.
4. The payment dialog opens and has the vendor filled in, todays date,
and the proper amount of the invoice I have highlighted.  I change the
Date (because these are old transactions) and enter the check number I
paid the invoice with in the Num field.  I select the Transfer Account
(Checking Account), and click Ok.  
5. I've had a few that post the whole transaction without a split in AP
and mark the Paid column with a check for that invoice.  However, more
times than not it does not mark the Paid column and I see very odd split
transactions in my AP.  The splits don't seem to make sense at all -
sometimes there are only two, sometimes several, and most do not match
any other single AP transaction.  
I'm confused.  I don't want a split at all - just want to pay an entire
invoice.  I can go into my AP, find the transaction, and Remove the
Split, but my invoice still does not show as being paid.

One thing I did notice is that my vendors invoice numbers are not in
ascending order for some reason.  Older invoices have a higher invoice
number.  Don't know if this matters. 

Any advice as to what I am doing wrong or what I'm missing?
-- 
Regards,

Fred