Your database appears to need patching to a higher level?

At the top of my homepage and admin homepage I have the following warning:

Warning Your database appears to need patching to a higher level. See Tools->Server Information to review patch levels.

I got this warning after upgrading my site to the new 1.3.9b from 1.3.8. Now I did look up this error on google to try to fix it myself, but I couldnt find anything helpful except people recommending that the installation needs to be finished. I know I finished the installation so I'm not sure what to do. Here is how I upgraded...

I decided to do a clean new install instead of upgrading my old files.
I find this prevents bugs better for me. So I backed up everything, SQL and all, and did a fresh and complete new install with 1.3.9b. That went good with no problems. I then changed my admin folder name to what it was and uploaded my original configure.php files. Still no problems at this point, so I upload all of my edited CSS files and other php files that just change the layout (none of them override the new 1.3.9b files). That went great so I import my saved SQL. Then I get this message I posted above showing. Well I figured it was because I still had to install the addons I had before, but after installing all addons I used before the message is still there. -_-

Any ideas on how to clear this error? Thanks a lot!

So upon further reading up on this it was recommended to put zc_install back on your site and run that to update your database again.

I just did this and it DID clear this warning...but now it has a warning on my homepage that says:

NOTICE: The website is currently Down For Maintenance to the public

and this warning on my admin site:

Warning WARNING: Site is currently set to Down for Maintenance ...
NOTE: You cannot test most Payment and Shipping Modules in Maintenance mode

??? Is this a new feature of 1.3.9 that I need to turn off that automatically turns itself on ???

After doing the database-upgrade via zc_install, you need to go into your admin area and remove-and-reinstall all your payment and shipping modules. This is documented in the upgrade instructions in the /docs/ folder of the Zen Cart files. After you've done that, you can turn off the down-for-maintenance by going to Admin->Configuration->Website Maintenance and setting Down For Maintenance to False.

Uh well I found where in admin you can set this "website maintenance" warning and turned it off. Totally not a new feature...I just never noticed it I guess because I use a test server. I never have our real site down for maintenance.

But back to the original problem. That first message

Warning Your database appears to need patching to a higher level. See Tools->Server Information to review patch levels.

It seems me clearing it with a reinstall of zc_install messed up my easy populate addon. So now I have to fix that as well.

Is there any other way to clear this warning other than the way I already tried? So I can avoid this problem in the future?

Thank you for your reply DrByte.

I only had 1 payment and shipping module and did reinstall them prior to importing SQL.

Salixia:

I only had 1 payment and shipping module and did reinstall them prior to importing SQL.
That's the backwards order.
If you're going to import an old copy of your database, then you'll need to remove-and-reinstall your payment/shipping modules after you run zc_install to upgrade the imported database.