FM 9: Cannot apply conditional tags

I've been able to create conditional text tags, apply them, and see the conditional indicators fine in several documents using FM 9. Recently, in a new book, I'm unable to apply conditional tags. I believe I've figured out the new UI, since conditional tagging has worked before. I can create tags and configure them fine, but when I apply them to text, a table, graphic, etc. nothing happens; the text remains unconditional.

What specific version of FM, as shown in Help > About?  What O/S and service pack level?
Does FM's built-in Comment condition work for you?
As a test, I'd suggest creating a small test file, create a new condition and apply it to some easily searchable text, e.g. "zzxy" or something, and also apply FM's built-in "Comment" condition to another piece of text,  then saving the file as MIF. Then look at the MIF with a text editor, or the excellent freebie MIFBrowser,
http://www.wideman-one.com/gw/tech/framemaker/mifbrowse.htm  
and search for the text. You should be able to see whether the condition(s) have been applied to the text correctly (or not), and also see how the conditions themselves are defined in the Condition Catalog entries.
Sheila

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