No .. this isn't a bug per-se. I'll bet that the alignment is lost before generating the book. After setting the alignment and saving/closing the file .. reopen it and see if the alignment is still there .. I'll bet it's gone. Typically, you can't apply formatting or properties to objects (elements) in a DITA file. This goes for font and paragraph properties as well as table formatting and other types of formatting. All you can do is create elements and set attributes. Any setting of properties will typically be lost on file save.
You'd likely need to have a "publishing process" (script of some kind) that you'd run on your generated book and chapter files which would scan for an attribute that would indicate certain properties need to be set on the table. The @outputclass attribute is typically used for this type of thing. I'm not aware of anything in default FrameMaker DITA that's set up to handle this type of formatting of tables.
If this formatting you're trying to apply is consistent for the entire table, it's possible that you'll be able to achieve this by creating a new table format that has this formatting set by default. When you insert a table in a topic, the table format is assigned to the tgroup/@outputclass attribute, and that's the formatting that is used when the table is rendered. Just create a new table format in the structured application template, and set up that format to have the properties you want. Then when you insert the table, be sure to select that format. It can be tricky to set this up but it *should* work.
However, if this doesn't work or you need more fine-grained formatting applied to table parts, I produce a tool called DITA-FMx that provides extended DITA authoring and publishing options for FrameMaker. It has features that allow this type of table formatting to be applied by setting the @outputclass attribute to a specific value on the row or cell. You can get more information on DITA-FMx here ..
http://leximation.com/dita-fmx/
Good luck!
Scott Prentice
Leximation, Inc.
www.leximation.com