Unresolved internal destination - tables and figures nottransforming

I'm FO 
transforming individual chapters of a book with Saxon 6.5.5 and not getting 
figures, tables and examples formatting properly in the PDF. I mainly get 
the text of tables, and figure captions, but mixed in with the body text 
(e.g. no table borders). Error messages are "unresolved internal reference" 
followed by the figure or table name. Transformation is inconsistent, as I 
am getting one or two figures formatting properly at the beginning or middle 
of the chapter but surrounding figures are not formatted.

I've 
tested the chapters individually before, so I know my stylesheets work and 
I'm referencing the images folder correctly. Any general suggestions on what 
to check, before I send through the coding examples?

Thanks,

 

Dave Gardiner