I went to look more closely at this, and it doesn't actually seem to be a data structure issue (some of the other merges that happen are the ones that are affected by this).
Can you debug org.broadleafcommerce.common.extensibility.context.MergeApplicationContextXmlConfigResource line 53 and see if the parameter arrays have the files in the correct order for you?
Edit: If you want to hop on IRC, we can probably figure this out faster - if this is a problem in Broadleaf, I want to get it identified and solved as soon as possible.
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