This seems to really have two parts to it and is why I found the issue. Basically the autoupdate popup and icon showed
up after I installed the update from the plugin manager tab, but read below and you'll see how the popup didn't show up
until I went into the plugin manager and had to tell it to reload the catalog. The steps follow:

1) In my IDE, I knew an update was available for a plugin I had installed as I had a message on another system. So, I
thought it would show up in my IDE after it started. This didn't happen.
2) I went to the plugin manager (Tools|Plugins) and the update did not show up until I told it to "Reload Catalog".
3) It then showed up in the plugin manager updates tab.
4) Not only did it show up in the plugin managers update tab, but the autoupdate popup message and icon showed up in the
IDE.
5) I installed the update from the plugin manager.
6) After updating the IDE asked if I would like to restart the IDE, and I told it yes.
7) It started going to work, and I decided to jump on my other computer and do some things while it worked on the update.
8) I went back to it long after the IDE had been restarted.
9) The autoupdate popup was still there showing and the icon which alerts the user updates are available (it looks like
the earth with an upward curling arrow).
10) I clicked on the icon to see what the 1 update available was.
11) It was the same update I had installed from the plugin manager.
12) The IDE read "your update will be updated" or something like it.
13) It then discovered the IDE was up to date.

Anyways, it seems the message should have been removed on restart or even after the updat was installed from the plugin
manager. In this particular case, though I have had to perform "Reload Catalog" before to see updates, the plugin to be
updated was the Axis2 support.