As far as I have seen, webmin and/or virtualmin caches the yum check-update info in collectinfo process, so, assuming you have those turned on, when they eventually run again, it should go away.
It has been stuck like this for over 6 months now. I was hoping it would be some sort of cache that may clear eventually but it has not so far. I was hoping that it may be as simple as deleting a cache file or folder that may cure it.
Yes I always update to the new releases when they appear & yes it is from the Centos Base. The source is listed as Updates.
Here is the response from /etc/yum.repos.d/CentOS-Base.repo
[root@sb2 admin]# cat /etc/yum.repos.d/CentOS-Base.repo
# CentOS-Base.repo
#
# The mirror system uses the connecting IP address of the client and the
# update status of each mirror to pick mirrors that are updated to and
# geographically close to the client. You should use this for CentOS updates
# unless you are manually picking other mirrors.
#
# If the mirrorlist= does not work for you, as a fall back you can try the
# remarked out baseurl= line instead.
#
#
[base]
name=CentOS-$releasever - Base
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=os
#baseurl=http://mirror.centos.org/centos/$releasever/os/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5
#packages used/produced in the build but not released
[addons]
name=CentOS-$releasever - Addons
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=addons
#baseurl=http://mirror.centos.org/centos/$releasever/addons/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5
priority=1
#additional packages that may be useful
[extras]
name=CentOS-$releasever - Extras
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=extras
#baseurl=http://mirror.centos.org/centos/$releasever/extras/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5
priority=1
#additional packages that extend functionality of existing packages
[centosplus]
name=CentOS-$releasever - Plus
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=centosplus
#baseurl=http://mirror.centos.org/centos/$releasever/centosplus/$basearch/
gpgcheck=1
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5
priority=2
Good news, looks like you hit the nail on the head there.
I had excluded the package using /etc/yum.conf which worked perfectly for yum via command line. It seems wm/vm does not use the excludes in that file.
So I added the line Exclude=mysql to the repo file as you suggested and did a package refresh inside wm/vm and it disappeared. It was still on the main system information screen so clicked on refresh modules and it went away there too.