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How can a stop my system folder from opening on startup? I checked the startup folder and it is empty.

That's unusual. Type msconfig in the Run box and first look in the Autoexec.bat tab to see if c:\windows\system gets a mention.
If not look at the Startup tab and see if there is anything similar there. It is safe to "temporarily" disable anything except ScanRegistry (just to find the culprit).
There are other ideas (registry & viruses) but check these out first.
.... oh yes, check also here:
c:\windows\all users\start menu\programs\startup.Anything appearing in the last folder (startup) will run when you start your machine.
DerekW

Although this article refers to NT class, Check these two registry keys:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run
Each named value within these two keys represents a program launched at start-up; each value's data holds the command to be executed. If the command is blank or contains just a character in double quotation marks, this missing data can cause Windows Explorer to display the System32 folder at start-up.To fix the problem launch REGEDIT from the Start menu's Run dialog and navigate to one of the keys mentioned above. Select Export from the Registry menu and export the key to a REG file, so you can undo any deletions if necessary. Look carefully at each value in the right-hand pane. If the value's data is blank, contains only single quotation marks, or otherwise appears to be corrupted, delete the value. Repeat the process for the other key, then restart your system to verify that the problem Explorer window does not appear at start-up.
Ref:
http://www.pcmag.com/article2/0,1895,1401312,00.aspBest

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