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You are unclear by what you mean by annotations.
If you annotate the image the text is part of the image, so you can't 'loose' the text!
It sounds to me that it is more likely that windows is adding an extra 'meta-tag' to the TIFF image (which is a hack of such meta-tags). Naturally IM does not understand or even try to understand all these extra unknown tags.
I suggest you annotate the text with IM so it gets directly drawn onto the image rather than saved as meta-tag.
Hmmm... have you looks at the identify output?
Many formats have 'comment' and 'label' tags that IM does understand. See the montage examples where I read and use this meta info to set montage labels. See the end of this sub-section of examples
http://www.cit.gu.edu.au/~anthony/graph ... age/#label
Their I set a 'comment' in three image formats, and then display the comment in a montage of those images.