@elfnor: You are probably hitting a path-length problem. When creating a file, calibre has to make sure that it has a legal file name. This includes making sure the full path is not to long. In Windows, the limit is 256 or 260 characters and I don't remember if similar limits are used on the other platforms.
When the path is to long, and this includes the directory you are saving to, calibre fiddles with the parts of the path to reduce the overall length. The examples you have are the type of changes I have seen.
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