Have a look into /proc/key-users to see if user root reaches its quotas:
0: 1029 1028/1028 10/100 2345/20000
means that root uses 1022 from 10000 possible an uses 2345 bytes from maximum 20000.
You may have to encrease both. For each user and group you should increase it by one. So if you 1000 users and 1000 groups you should root allow more than 2000 keys (and enough memory for that).
Have a look into /proc/key-users to see if user root reaches its quotas:
0: 1029 1028/1028 10/100 2345/20000
means that root uses 1022 from 10000 possible an uses 2345 bytes from maximum 20000.
You may have to encrease both. For each user and group you should increase it by one. So if you 1000 users and 1000 groups you should root allow more than 2000 keys (and enough memory for that).
Try
echo 400000 > /proc/sys/ kernel/ keys/root_ maxbytes kernel/ keys/root_ maxkeys
echo 10000 > /proc/sys/
and see if this fixes the problem for you.