2 save location's keep calling eachother

I have two labview projects saved on my computer. One is our code which we have as our base code which we are not going to be editing. The other is the one which we are changing and using for the competition this year. When I try and load one (as of right now they are the same code due to some other computer errors) it is asking me to determine where to call the global variables from. When I try and switch between the codes the global varibles are called from the perviously used file, even though they are different locations. Is this normal when two codes are saved on the same device and if not is there any way to fix it?

Are you using project files?  If not, you really should.  They help a lot keeping your different projects separate.
Your problem is that your VIs from the different projects have the same.  It is very easy to get "cross linking" in this situation.  Setting up the project files will help a lot to alleviate this.
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    GPSVC(410.1730) 09:10:51:186 ProcessGPO:  ==============================
    GPSVC(410.df0) 09:10:51:186 GetGPOInfo:  ********************************
    GPSVC(410.1730) 09:10:51:186 ProcessGPO:  Searching <cn={DC3C93EC-7C28-48E9-BA38-FCA1E275A207},cn=policies,cn=system,DC=gc,DC=local>
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    GPSVC(410.1730) 09:10:51:191 GetGPOInfo:  ********************************
    -------gpsvc.log start---------
    -------output of gpresult /r-------
    Microsoft (R) Windows (R) Operating System Group Policy Result tool v2.0
    Copyright (C) Microsoft Corp. 1981-2001
    Created On 5/30/2014 at 9:24:08 AM
    RSOP data for GC\ssanders on OPTI9020-01 : Logging Mode
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    Site Name:                   Default-First-Site-Name
    Roaming Profile:             N/A
    Local Profile:               C:\Users\ssanders
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    -------end gpresult output-------       
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