Issues w/ notes when importing Word files; better as RTF?

Hi,
I've always had issues when importing Word files into InDesign CS4, and after just getting CS5 it seems that they haven't been eliminated. Since it looks as though I'm going to have to just deal with these issues (I have to accept Word files from a wide variety of sources, so I can't move to an InCopy workflow, unfortunately) I thought I'd ask for some advice.
After reading some suggestions on this forum I began making sure to accept all tracked changes and then saving to a .docx file before importing. But I have still been having trouble with disappearing endnotes (ie all notes in the text up to a certain number just get lost, even though the references at the end of the text are complete); and often the first note (the reference, not just the number) appears in an anchored text box within the text. Disappearing note numbers are the most frustrating, because it's easy to miss until much later in the layout process. Is anyone else having these problems? In fact, in a few cases saving to .docx seems to -cause- more problems than it solves.
In any case, it seems that saving as an RTF file can produce better results, but I'm a bit wary about doing this all the time in case information gets lost when moving to RTF, or in case there are problems that I just haven't noticed yet in importing RTF files.
So, long story short, is there any reason I -shouldn't- save all my Word files as RTF files to avoid problems when importing them in InDesign?
If anyone has other suggestions for steps to follow when importing Word files (besides dealing with tracked changes and saving as .docx or RTF) please feel free to mention those as well!

I don't know much about your particular case (endnotes) so I can't offer much in the way of specific advice. I also don't know where your Word files are coming from, but for me the best workflow is when
1) I make an ID template
2) I export an RTF from that template
3) People use those RTF templates in Word and fill 'em with text
4) People send me Word-edited RTFs
5) I place those RTFs
It's useful to know what you will lose when going from DOC -> DOCX -> place in INDD
or
DOC -> RTF -> INDD
but the only way to know for sure is to test with your content. Some things break when saving to RTF from Word, but I've found that those things are mostly Word-specific stuff that I wouldn't want in any file to be placed in ID. Text boxes, WordArt (faugh), other things that MS has spot-welded onto the side of their word processing app.

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Thanks Sheila, have now overcome my problem with editing the post (duh!)
Hope the below is clear enough as cannot send an actual screen shot. Have discovered that the number of directories above in path is a red herring because the problem now happens back on the original pc when the book and files are copied back to it.
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Subject: FrameMaker General Discussion Part of path lost when importing autogenerated files
It would be really helpful if you might do a screenshot of the File Manager hierarchy of folders and insert them into your posting, maybe use callouts to annotate the various significant levels -- a visual would really, really make it much easier to interpret what you're describing.
>
Sorry, not coming out very clear compared to viewed on PC. Directories are A, B, C - Dir A caption "The Directory above the content directory. Links in the subset book in Directory C look in here after they are imported into other files in the subset book"
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Directory C says "Directory C containing the subset book with its own index, LOT, LOF, plus links to introduction, glossary/index and a couple of other files in Directory B. The links to files in Dir B work in the autogenerated LOT, LOF etc, but not when imported into content files (linked files in directory B) although this used to work. They now look for the content files in Directory A instead"
Hope that makes it clearer.

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