I can't open batch files in windows 8.1

I am trying to run a batch file in windows 8.1, when i run the batch file runs at first but closes so fast that you can't see its contents, you can't even see if its doing what you tell it to. Since the file does run but closes fast, i thought of adding
pause. Adding pause did not fix the problem. I am not sure if i have to change my keys on regedit, or i have some kind of malicious software that needs to be fixed ( I think i have no malicious software, i have run security scan many times
nothing showed up, I had a Trojan horse, Trojan.Gen2, long time ago but the Trojan got quarantined?) I originally had windows 8 but upgraded to windows 8.1.
Help Please! I don't Know what to do!!!

Hi Glogikon,
"I am trying to run a batch file in windows 8.1, when i run the batch file runs at first but closes so fast that you can't see its contents, you can't even see if its doing what you tell it to."
According to my experience ,it is a normal symptom .Did the bat file run well before ?
Have you tried to run the command one by one in the bat file from a command line ?Have you tried to run the other bat files which including a output to have a check ?
If it is possible ,please post the command of the bat file here .We will make a test for you .
To check whether the bat run well ,this link may be useful:
check if command was successfull in a batch file
http://stackoverflow.com/questions/14691494/check-if-command-was-successfull-in-a-batch-file
" I think i have no malicious software, i have run security scan many times nothing showed up,"
We can try to work with the following official free tool to have a check .It is recommended to run it in a safe mode to improve the quality of the scanning.
Malicious Software Removal Tool
http://www.microsoft.com/security/pc-security/malware-removal.aspx
NOTE: This response contains a reference to a third party World Wide Web site. Microsoft is providing this information as a convenience to you. Microsoft does not control these sites and has not tested any software or information found on these sites.
Best regards
Please remember to mark the replies as answers if they help, and unmark the answers if they provide no help. If you have feedback for TechNet Support, contact [email protected]

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