Hello, MJP.
We don't have any known issues like that with BookMacster 3.0.3.
1. Not common, but it you have BookMacster on more than one Mac or are using anything else to sync Safari to Chrome, ensure that you do not have a
sync loop.
2. Your Safari bookmarks in iCloud, or maybe Chrome bookmarks in the Google cloud, could be on the fritz. The short version of how to fix that is
Switch off syncing.
Get all of your bookmarks into BookMacster as desired.
Delete all items in Safari and Chrome bookmarks.
Wait an hour or so, or maybe as you say "so often" and ensure that no items reappear in Safari or Chrome. If they do, delete them and repeat.
In BookMacster, export to Safari and Chrome, or enable syncing if desired and export to Safari anc Chrome as prompted.
We also have a
more detailed version of those instructions, for Safari only. I've never seen this issue with Chrome, but you may as well do both at once.
(Since we occasionally need to help people with stuff like this, I'd appreciate a follow up so we can increase our expertise and increase out insight into the black box of Apple's iCloud Safari syncing.)