Your comments

That feature could be combined with http://roadmap.cintanotes.com/topic/15284-saved-predefined-searches/ . Your request could be implemented by allowing to define, which saved search should be used as an initial filter.
Chris, the link to "this request" is broken. It should read http://roadmap.cintanotes.com/topic/116796-tag-relations-explorer/ .
Yes, my suggestion is an additional view to the tag-sidebar. Your suggestion is different, because it is the list view that is shown by groups. I like that and have just voted for it. Both requests share the fact, that a note can appear in the list more than once. PS: You should add that image to your request for it makes the suggestion clearer. 
Chris, not sure i understand your question. With todays tag-sidebar you'll always have all notes listed, that fulfill the tag filter. That is pretty much the same with the relations-explorer. However, in the tag-sidebar related tags should be grouped. The filter is actually the same as with the classical tag-view. E.g. when you click on "customer-A" you'll get all notes listed that have that single tag assigned. When you click on "customer-A/project-A" you'll get all notes having both tags assigned. I think the resultset, the notes listed is the same as with a regular search. The difference is, that with the classical tag-sidebar you filter on tags explicitly. With the relations-explorer you browse an automatically generated tag-tree having the tags filtered implicitly.
I think what Andrew asked for can be done with my request for a tag-relations-explorer; check here: http://roadmap.cintanotes.com/topic/116796-tag-relations-explorer/ .
Andrews example can be shown as:
  • Music
    __My-Works
  • My-Works
    __Music
    __Architecture
  • Architecture
    __My-Works
    __My-projects
    __Famous-Buildings

This all can be done with the use of "flat" tags or as Andrew calls it "zero-level" tags.

Example:
  • customer-A
    __project-A
    __project-B
    __projects
    __software
  • projects
    __project-A
    __project-B
    __customer-A
    __software
  • software
    __project-A
    __project-B
    __projects
    __customer-A 
Imo the issue should be declined. If this is really of interest it should be a feature request, not a bug report.
Sorry Mark, i did a second test using WordPad. This time with editing an existing note. Still can't reproduce.
Mark, i tried to reproduce, but it works fine here. Which editor did you use to edit the file? Maybe you damaged the settings file? In that case you would need to restore the file. I edited the file myself using Windows\Start and typed "editor".
The reason for this request is, that i want to have a hierarchical view on the data, while at the same time assigning only "flat" tags. It is also important to me, to look at the data from different angles. For example i can look at "project-A" coming from "customer-A" or "projects" or "software", depending on what my current perspective is. Imo this is a feature no other outliner software supports, yet it is very powerful.