Whenever I post a flash on a website it comes up with a white box around it, on
PCs only. It goes away once clicked upon, but i was wondering if there was some
script that would make it be gone automatically that i could add. Please let me
know.

Flash CS3 has the activecontent html template as its default which fixes this.

If you have flash 8 check this out:
http://kb.adobe.com/selfservice/viewContent.do?externalId=7c29e252&sliceId=1

I used SWFObject as my preferred javascript replacement method. Its here:
http://blog.deconcept.com/swfobject/