Are the files that open differently detected as the same mime type?  

XML is used for lots of things, and the mime type detector can tell them apart 
from the contents, there is not one "XML" type, see 
[here](https://en.wikipedia.org/wiki/XML_and_MIME).  And each mime type can 
have a different opening command configured.

If they are different mime types they may have different geany commands 
configured?

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