My client is using Softaculous for software upgrading. I tried upgrading from the WordPress dashboard and it wouldn't let me. Do I have to somehow "uninstall" Softaculous for this to work?
Softaculous doesnt configure anything in WordPress which would stop a Manual Upgrade. You can contact the support team and they should help you. To test your claim I just upgraded my Blog which was installed by Softaculous and it is working. You should check for the PHP error logs as well.
You can simply upgrade WordPress using Softaculous :
This page will guide you in Upgrading the Scripts and getting the latest version available by Softaculous.
You might need to talk to your client's host. The problem could be a server configuration issue, or it could be a problem with how Softaculous configures WordPress.
A quick Google search doesn't turn up any obvious problems with using the core upgrade mechanism with Softaculous-installed WordPress. You might need to reference one of these Codex entries: