There were absolutely no database changes between 1.6.0 and 1.6.3 at all, apart from having some templates updated. So, if there's a problem on your 1.6.3 database but not your 1.6.0 database, it must be something like a table index has gone missing; if you're still using 1.6.3 files then it's obvious that MyBB is not the cause, the databases should be exactly the same.
Hello again,
from what you said, the problem (for me) is missing of table index.
But how this happens? I have done all the steps of upgrade without any problem.
Do you advice me to wait and upgrade to the next version 1.6.4 when it releases?
And regarding my server load, it drops alot when restored to 1.6.0.
with 1.6.3: CPU usage 120-200 %
with 1.6.0: CPU usage: < 100%
And i have restored 1.6.0 files.
Well, the upgrade script doesn't touch your indexes in any way. Just upgrade to 1.6.3 with 1.6.3 files (going back to 1.6.0 stuff is going to make it impossible to debug) and list what indexes all your tables have. if this happened when going from 1.6.0 > 16.3, waiting to upgrade to 1.6.4 won't do anything as the upgrade isn't what would have caused your indexes to disappear.