We found the issue, a piece of HTML was being rendered in a Dynamic Label and the HTML was corrupted, most likely by tinyMCE (a HTML editor). For more information see http://www.electrictoolbox.com/tinymce-mcepaste-divs-webkit-browsers/. A possible solution is to look for id="_mcePaste" in your custom HTML content and removing it before generating a document template.
The error is generated by the following part of your stacktrace:
Caused by: com.mendix.systemwideinterfaces.MendixRuntimeException: javax.xml.transform.TransformerException: org.apache.fop.fo.ValidationException: Property ID "_mcePaste" (found on "fo:block-container") previously used; ID values must be unique within a document! (See position 13:125)
Nov 16 13:56:20 127.0.0.1 dsitest: ERROR - Connector: (8/100) at lr.a(SourceFile:100)
Nov 16 13:56:20 127.0.0.1 dsitest: ERROR - Connector: (9/100) Caused by: javax.xml.transform.TransformerException: org.apache.fop.fo.ValidationException: Property ID "_mcePaste" (found on "fo:block-container") previously used; ID values must be unique within a document! (See position 13:125)
It appears that you are using the same IDs (name in your property tab) for components on your document template that you are generating.