I should add: The app reads the problematic table with no problems.
I have discovered the problem is with a method anotated with @PostPersist and @PostUpdate. If I remove these annotations the problem goes away!
Again: this works fine in with MySQL
Enable SQL logging and see what query gets fired. You might then take the help from a DBA to monitor why the table gets locked.
I am closing this since it is somewhat miss-labeled now that I know more about it.
Search for SLSB and MSSQL and Entity to find new post.