Skipped Upgrade Statements

Ver 1.3.8
Trying to upgrade to 1.3.9
No addons

Having tried unsuccessfully to find an answer for this, I must ask the forum for help.

I have done all the initial steps for upgrading from 1.3.8 to 1.3.9 and am now attempting the actual upgrade, but I keep getting the following error:

NOTE: Skipped upgrade statements: 3
See details at bottom of page for your inspection.
(Details also logged in the "upgrade_exceptions" table.)
Note: In most cases, these failed statements can be ignored,
as they are indications that certain settings may have already been set on your site.
If all the suggested upgrade steps have been completed (no recommendations left),
you may proceed to Skip Upgrades and continue configuring your site.

This is what is being skipped:
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot insert configuration_key "SHOW_SPLIT_TAX_CHECKOUT" because it already exists
SKIPPED: Cannot add index idx_prod_id_orders_id_zen to table orders_products because it already exists.
SKIPPED: Cannot add index idx_cust_id_orders_id_zen to table orders because it already exists.
SKIPPED: Cannot add index idx_cust_id_orders_id_zen to table orders because it already exists.
SKIPPED: Cannot add index idx_cust_id_orders_id_zen to table orders because it already exists.
SKIPPED: Cannot add index idx_cust_id_orders_id_zen to table orders because it already exists.
SKIPPED: Cannot add index idx_cust_id_orders_id_zen to table orders because it already exists.
SKIPPED: Cannot add index idx_cust_id_orders_id_zen to table orders because it already exists.

I went to my upgrade extensions log and saw the details, but I'm not sure what to do.:unsure: I tried deleting them from the log, but they come back again when I try to update again. Does anyone know how I get rid of them, ignore them or fix them so that I can complete the upgrade?

Your Error states:

twofair:

...
NOTE: Skipped upgrade statements: 3
See details at bottom of page for your inspection.
(Details also logged in the "upgrade_exceptions" table.)
Note: In most cases, these failed statements can be ignored,
as they are indications that certain settings may have already been set on your site.
If all the suggested upgrade steps have been completed (no recommendations left),
you may proceed to Skip Upgrades and continue configuring your site.

If you have done everything by the book then you can continue ...

You are right. I thought that it would notify me that all was finished and give me the option to go to the store or admin, so that is what I was waiting for.

The site is up, but it looks like the original zen cart store; none of my changes are there even though I added my override files as instructed. This is my fourth attempt at upgrading; even had someone overseeing as I did each step to make sure I was doing as instructed, but it still isn't "working" - meaning it doesn't reflect my design/text changes. I don't have any addons, just about 10 or so files I used the override system on, my images and my content.

I only have 7 products, no customers yet. Would it be best to just start with 1.3.9 from scratch and make the changes one by one? Is it really that difficult to upgrade or am I seriously missing something important here?

Okay, posted too soon on that last one - didn't check my files thoroughly. I added my overrides, images, etc. via WinMerge, uploaded the files to my server and did the upgrade. The files I added and the changes I made are not there - hence the sitestill looks like original zen cart. Why aren't my changes there? Did they get booted out with the upgrade? I know it's hard to believe, but I have been following each step - measuring twice, cutting once. What am I missing?