Recently, the following note is released:
'2250883 - Custom theme does not appear as expected after server restart'
This note relevant from: '731 sp16/740 sp11' and up and in case of using LESS theme structure(with theme designer tool).
This note about following issue:
After restarting the portal server or restarting the LAF service, custom themes are not working as expected.
As a workaround the administrator can rebuild the theme in theme designer but after restart it's stop to work well again.
For getting the fix you can apply the patch mentioned in above note