Can't use external JavaScript file in a different directory, only when using WAMP

This is a follow up to this question. In WAMP I've got the www directory containing the directories alpha and bravo. A JavaScript file is in alpha and a HTML file that includes the JavaScript is in bravo. WAMP seems to have a problem with this, whenever I call a function defined in the JavaScript file it says it's undefined but if I copy the folders to my desktop it works. Is there something going on with permission here?

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If you are talking permissions, the first thing I would do is make sure your .htaccess file is up to scratch, and see if these folders have their own .haccess permissions. –  Alastor Feb 13 '13 at 22:49
I never made any .htaccess files –  Celeritas Feb 13 '13 at 22:51
Ah right, without them WAMP runs it's own default modules which might be causing issues. Also are you calling the file through path (like C:\folder\folder\alpha) or relatively (like ..\alpha\js.js) ? –  Alastor Feb 13 '13 at 22:56
Relatively. So ../alpha/aScript.js (at this point I made a test project so the names are bs) –  Celeritas Feb 13 '13 at 22:58
@Alastor how do I change the default modules? –  Celeritas Feb 13 '13 at 23:00