Ehi!
How many markers you’re trying to save?
I’m asking because by default php save 1000 record at a time.
Considering the fact that main settings, subdivisions and markers fields are sent as a whole, probably you reached this quota !
I tried this plugin
which basically alerts you when this limit is reached.
Here an explanation on how to solve it via php.ini or via htaccess file.
Newer versions of PHP implement a php.ini directive called max_input_vars usually set to 1000. This means that posting > 1000 form fields for instance would be truncated preventing data from being saved.
This can be changed in php.ini:
max_input_vars = 2000
If you need to do this via htaccess (on a shared host for instance) you may use:
php_value max_input_vars 2000
This is the page where I’ve got the workaround above : https://docs.woothemes.com/document/problems-with-large-amounts-of-data-not-saving-variations-rates-etc/ ).
Please let me know if you are able to solve it.