Unwanted Command Prompt

I have a Win 7 Pro 64-bit system that has been working fine. The other day I noticed after the boot up sequence had finished after about 60 to 90 seconds an elevated level command prompt pops up. I'm having trouble finding what is causing this.

It doesn't appear until the windows start up is finished and I have a usable GUI. It doesn't have any effect on anything and there isn't anything showing in the command prompt list .. I've attached a screen capture.

I can close the window and be done with it, but it will always come back when ever I turn on the computer or re-boot it. I've been playing with disabling various start up programs and processes but have not yet found what it is or more importantly what is causing it.

As a precaution I did extensive virus checking and such .. everything looks normal. The only other odd thing that happened around the same time was that my MS OFFICE suite disappeared. I have a open source version of office that I no longer use but still have on the PC, and one day when I opened an Excel spreadsheet it automatically opened in Open Office.org .. instead of my MS Office. Then I found that my MS Office 14 folder was empty .. Also found over 800 bad registry entries that may have been due to my MS Office suite being deleted from the hard drive. Sort of what you get when you delete an application without un-installing it first.

So of course my first thoughts is that the two problems may be related and maybe my PC was hacked or something.

I'll reinstall Office but am concerned about this command prompt that keeps appearing ..