I presume that the different applications don't use exactly the same formatting rules and thus it cannot work properly.
I have the same kind of problem if I highlight things in a same book in my Kindle app and also in my Kindle device. One added functionnalities on the app overlap the highlighting function in the normal Kindle device and create bugs.
Depending on the devices you can find help here :
Mac - Windows - General support
I advise you to be very specific in your questions there (which devices are used, application version, give files as examples).
If you don't find then maybe you must limit yourself to only one main device (or at least have the exact same configuration between a workstation and a laptop by example). The last option would be to work on an alternative of Scrievner