Speaking as an IT guy -- just not your IT guy -- I'm sorry to say that it sounds like you are, in fact, infected.
The STO launcher uses some parts of Internet Explorer (which is why it works funny, if at all, if you somehow manage to completely remove IE.) Some viruses hijack IE system calls and will open up a variety of windows, either to generate hits or to get you to click on something you shouldn't or any number of other reasons.
Since nobody else has reported STO exhibiting the behavior you describe, it is a safe bet that you have been infected. boot into safe mode with networking, download Malware Bytes*, install and run. Then run again. Then just to be certain download and run (while still in safe mode) TDSS Killer*. Then reboot and install MS Security Essentials*, Avast!*, or AVGuard*, or spring for Kaspersky*.
Of course the only way to be absolutely certain your machine is not infected is to replace the hard drive, and reinstall the operating system.
If any of this confused you, I recommend talking with your IT support person, whomever that may be.
Also? Once your computer is clean, if not sooner, change ALL your passwords. ALL OF THEM. It's the only way to be sure the bad guys didn't get anything belonging to you. And keep an eye on your credit card statement for the next few months.
* - I am not associated with any of these products or their companies, nor do I explicitly or implicitly make any guarantee their success.