Smart groups empty following upgrade to 4.6.20 or 4.6.21

There is an issue we found on this version. There is a warning message appearing in Manage Groups saying that Smart group contacts are not getting counted. In the list they really are not counted, all smart groups have 0 contacts. But if you open the Contacts link, all the contacts appear, and checking the Manage Groups list, the opened smart group's contacts get counted. However when you clear the caches in Civi, all goes back to 0.
The "Update Smart Group Counts" is not working. After clicking that link, the counts are still 0.
This is the case on our client sites and my local site as well.

Steps to recreate:
1. clear caches in Civi
2. go to Contacts/ Manage Groups
3. the warning message should appear at the top right corner
4. check the Smart groups' Count column --> its 0
5. click one of the Smart Group's Contacts link --> the contacts do appear
6. navigate back or open the Smart Groups menu again --> the smart group you opened in step 5. should show the relevant number of contacts
7. check the other smart groups in the list --> they are still having 0 in Counts column
8. clear caches again and check the Manage Groups again --> the warning message appears again and all Smart Groups have 0 counts