The problem was fixed as of version 5.04 and we have verified that the problem is not present in the latest version, which is version 6.05.
That is the version I have. I have also tested using a very short path and it did not fix the issue. Could there be another reason for this issue?
I just did more test on this. I have two document files in the same folder. Their annotation files are also in that same folder. The annotation setting for one document is preserved but the other is not. So, it looks like an issue not with the path but with something else. Could anyone please help? Thank you.