In the meantime I probably found the reason but for this I need to explain 
a bit more.
The test case is running on multiple threads, each thread has his own 
connection to the database.
Each thread listens to a MQ queue for getting messages.
For each message two merge statements are performed, the second merge is 
always on the same record.

When not using auto commit I see H2 method 
org.h2.command.Command.filterConcurrentUpdate using a lot of cpu time in 
performance monitoring.
When using auto commit filterConcurrentUpdate isn't called at all.

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