When a new taxonomy is added to a CPT. When you add options to that taxonomy through the taxonomy section or the new CPT page they do not appear to be added after clicking the 'Add New xxx' button, but if the page refreshes then you see the new options added.
Look at the screenshots.
Thank you for contacting Toolset support. I am not able to reproduce this issue at my end.
1. Please also try to check it by deactivating all third-party plugins (except Toolset) and switching back to the Default Theme (e.g. Twenty Sixteen theme) to see for any possible conflicts with any of the plugins or themes?
2. Please also check browser console is there any error?
3. MySQL 5.5.5 version in your site, is lower than the required for Toolset. Please upgrade MySQL version and see if this resolves the issue: https://toolset.com/toolset-requirements/