To anybody who may have found this on google because they are experiencing this issue, since I am, while using Adobe CS6, 3 years after this was posted, the problem isn't that the loop function doesn't work, but rather that Encore's built in preview mode doesn't show the loop. In other words, if you build the project, it will work, if you preview it in Encore, it won't. 
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Re: Encore CS4 Loop Point goes back to beginning
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