Seems on the initial scan SecureAPlus marked MSE (Microsoft Security Essentials) as an Untrusted Program. It did this without any interaction.
I had to open Windows Explorer and go to the MSE folder and right-click on MSE and add it as a Trusted progrm in SecurePlusA.
Since downloading and installing SecurePlusA I noticed MSE hadn't updated in the week following the installation.
I'm only posting this in case anyone is tearing there hair out waitning on MSE to Update. I'll update this thread if any (or no) problems occur now that I appear to be Updating MSE