During the development of a big fat SharePoint solution which rolled out site columns, content types, lists and pages and linked all the relevant bits together, I came across a frustrating issue. When I was uploading a custom document content type on a library it was always defaulting to the Document (or default) content type after the item was uploaded. I found this blog post which gave me some ideas but after re-creating the document library and re-adding the content types but I still had the same problem. The issue was due to a “faulty” field in all of my content types. I had done the ol cut-and-paste for some of my field definitions and had a [NumLines] attribute associated with a date field. Narf. Removing this attribute and recreating the field resolved the problem.
If you are noticing something like this when uploading Word documents but it is not occuring with other types of documents- such as a PDFs, try clicking New -> Content Type on the library menu so that Word is launched , and make sure you have the Document Information Panel displayed. If there is a problem with one of the metadata fields then you might see some kind of error here which could identify the culprit.