Azure supports 2 types of storage, Page, and Block (you can read in detail on each here - https://msdn.microsoft.com/en-us/library/azure/ee691964.aspx
Cloud Xtender only uses Page Blob storage. With this type of storage, data is stored in 512 byte pages, so when a file is uploaded, it is padded out to a 512 byte boundary (i.e. if you copied up a 318 byte file, it is padded out to 512 bytes etc). If you were to then copy this files directly from the storage service, you would end up also copying down this padding. As a result, you need to manage the file via Cloud Xtender or another app that can read the file metadata (the metadata contains the files true length).
If you are unsure of what this all mean, we recommend you do not use Azure with Cloud Xtender.