SQL Server 2008 r2 sp1 upgrade?
one of the databases, I got "Failed to flush the commit table to disk in (dbid) due to error 2601." and the error log showed "error 3041 severity 16 state 1".


The above error occurs when you have CHANGE TRACKING enabled on the database. To find what databases have Change tracking enabled, run below tsql:

SELECT d.name AS 'Database Name', ctd.*
FROM sys.change_tracking_databases ctd
INNER JOIN sys.databases d ON d.database_id = ctd.database_id


This error was fixed in SQL Server 2008R2 SP1 +CU1.  Even with SP1+CU1, you are running an unsupported patch of SQL Server. I would suggest you to apply SQL Server 2008R2 SP3 then Security Update - KB3045316.


  A security issue has been identified in the SQL Server 2008 R2 SP3 that could allow an attacker to compromise your system and gain control over it.


Recommendations :


Take full backup of current databases with CHECKSUM.
Apply latest SP3 + Security Update (as mentioned above)
Stop using maintenance plans and use a more reliable backup solution (hint: Ola Hallengren's backup solution).