Normally when my webroot is doing a scan it runs thru the files pretty fast and even if it comes to a large file it only stays there for a few seconds and then proceeds on. However, now it comes to a particular file and just stays there. The timer icon keeps showing how many minutes have elapsed and the green bar keeps moving but the box that shows the names of the files being checked just stays on one particular file and that is - C:program files\java\jre6\lib\deploy\jqs\ie\jqs_plugin.dll. Why is this happening?

There might be a conflict

Background b> Many personal computers connected to the Internet will more than likely eventually become infected with spyware, malware, viruses or Trojan horses. Such programs spread via spam, bad links or freeware. Once they invade your computer, they can do anything they want, such as disabling your antivirus software, tracking your keystrokes and deleting files. b> About McAfee and Webroot b> McAfee and Webroot are some of the most popular computer security programs. Both companies have features on their programs, such as firewalls and live scans, which prevent future infections. Computer owners, however, should never run two programs since they cause each other to crash. Only one antivirus program should be on a computer at once. b> Spyware Prevention b> Along with using computer security programs, computer owners can prevent infections by browsing the Internet with caution. They should avoid file sharing and ad-laden websites since such websites often harbor spyware. They should also avoid downloading anything without researching it beforehand use as safe a Web browser as possible. If you right click in the bottom toolbar select task manager under processes and the applications tabs you will see what is running and ticking over if you see something running that should not be select end now or even uninstall it or disable it Hope this helps

You may need to reinstall it to fully uninstall it. The uninstall may not have worked.
Have you turned off your computer since uninstalling Webroot? (Fully turned off, not hibernation mode) That may get rid of the running file.
To finish the job after uninstalling, simply delete the directory from the C: drive. (You may have to turn off and restart the computer before it will allow you to delete the folder.) A lot of programs that download updates on a regular basis will leave the updates on your hard drive even after an uninstall.

What type? Please describe. However is the error is upon installation here are some tips:

The Windows Installer Service is required to install Spy Sweeper/Webroot AntiVirus 5.8 or Spy Sweeper/Webroot AntiVirus/Webroot Internet Security Essential 6.1. However, by Microsoft's design, the Windows Installer in not available in Safe Mode. On rare occasions Safe Mode installation is still desirable, so Webroot has engineered a method to make this possible. This method uses a file called "SafeCore.exe".

If the installation is performed using "Safe Mode with Networking" and an active internet connection is available, the Version Guard feature of our installer will automatically download and run SafeCore.exe. No action on the part of the user is required. Otherwise SafeCore.exe will need to manually be placed in the same folder as the standard Webroot software installer.

(Example: if the installer file is already on the Windows desktop, copy SafeCore.exe to the desktop as well, and then run the Webroot AntiVirus/Spy Sweeper/Webroot Internet Security Essentials 5.8/6.0 installer to begin the installation process).

To obtain a copy of SafeCore.exe, please first check what version of the Webroot software you are trying to install. Right click on the installer and choose Properties, and then click on the Version tab. A File version will be listed.

• If the file version is 5.8.1.55, please click SafeCore.exe to download the SafeCore files specifically designed for 5.8.1.55 and place it in the same folder that the installer is located in.
  
• If the file version is 6.1.0.128, please click SafeCore.exe to download the SafeCore files specifically designed for 6.0.2.22 and place it in the same folder that the installer is located in.
  

• If the file version is different than the two listed above, please contact Webroot Technical Support for an alternative option.
  

If the computer you are trying to install on does not have a network connection, it may be required to transfer this file from one machine to another using removable media such as a USB drive or CD-ROM.

If installing Spy Sweeper/Webroot AntiVirus/Webroot Internet Security Essentials 6.0, the Backup Component may not install completely in Safe Mode since it contains components that require the Windows Installer Service to install completely. You will need to re-run the installation in normal mode to activate the Backup component.

Usually a sign of Hard drive problems, boot up in safe mode if you can.
Right click on C: drive, properties/tools/error check and let it do a full scan with automatically fix errors chosen.
You may want to back up as much as you can if you manage to get into safe mode

Maybe some of your WW files are corrupted or not correctly installed . Here is my advice : Uninstall it and reboot system , then install it again and reboot and now it should work correctly .
good luck .

try going into your c: drive and Program Files and see if you see a folder for webroot or spysweeper.
delete any residual files and the folder.

you may have to go into your registry and remove the spysweeper keys, but unless you know how to do it i would let a pro do it.

you need to hit "ctrl alt del" hit task manager, then hit file->run and type explorer and hit enter

The scanner produces a "picture" of the document, much as if you laid it flat on a table and took a picture of it with your digital camera. If you did this, your .jpg from the camera would be several hundred K at a minimum - comparable to the file size off the scanner. That's why the file is so big, it contains a picture and not text data - even though it's still a .jpg file.
If you reduce the scan resolution you will save space, but at the expense of legibility of the document image. To get it down to the smallest possible size, you will need to run the scanned image through OCR ( Optical Character Recognition ) into a Word document for example, and then print it out to a .pdf file. If you have a clean source document with few graphics this isn't as difficult as it may seem. Microsoft Office has an excellent OCR process known as Document Imaging. You need to carefully proof read the result but with a clean input Document Imaging is amazingly accurate in Office 2007.
In short, there is no easy solution to your problem.

perform a custom sweep. you can do individual folder scans, and if you have files in question placed in this folder, you can scan just those files.

same problem.