IE window 1 pops up in front of IE window 2

Sounds like you have Adware.

Please do the following:

To check for a virus please visit one of the following sites for a free online virus scan. Even if you a virus scanner installed, this one gives you a second opinion, and it will be up-to-date which yours might not be.

Symantec:
http://security.symantec.com/sscv6/home.asp?j=1&langid=ie&venid=sym&plfid=23&pkj=TBOWYHGBYNCJEIMXQKC

Trend Micro:
http://housecall.trendmicro.com

If you do not currently have and antivirus program install you can try AVG from www.grisoft.com – it is free.

In IE go to Tools -> Internet Options -> and delete Files and Cookies.

To check for and remove any Spyware or Adware that may be installed on your machine, download and install Adaware SE and Spybot 1.3. Then update each program before scanning. Fix ALL problems found by either of the programs. You may need to reboot and have the scan run at startup. Run it again to make sure all components have been removed. There is also an Immunize in feature in Spybot that should be enabled to protect against some installations of Adware/Spyware.

Ad-aware and Spybot:
http://spywareinfo.com/downloads.php?cat=sp#det
OR
www.downloads.com

Then post a Hijack This Log to have someone analysis it for further cleaning/recommendations.

Hijack This:
http://www.spywareinfo.com/~merijn/downloads.html
OR
www.downloads.com

 

Oh, OK. This is normal. What you need to do is get Tweakui and set the "Prevent Applications from Stealing Focus" option. This is in the General Tab of Tweakui in Control Panel.

http://www.download.com/Tweak-UI/3000-2341-2830963.html?tag=lst-0-1

To install you must right click on the tweakui.inf file and choose install.