Setup Issues 

    
    NOTE:  recommended to Change workspace when upgrading versions:

Missing Icons - ie "Load Editor" icon missing - change location of workspace, eclipse uses the icon layout saved in the workspace

Workspace      - default :
                                      C:\Documents and Settings\[user]\dboptimizer\workspace 

                         [user] is the current user on the machine. (on windows)

                        Change  with:
                                              “File->Switch Workspace->Other…”

When changing workspace, you can add your old  SQL Project to the new workspace by
    right clicking in the SQL Project tab
    choose, "new" 
    uncheck "use default location"
    browse to the directory of your old workspace/SQLproject

Opening Saved Files  - various way

•  windows: drag file from Windows Explorer into DB Optimizer
•  File -> Open File
•  SQL Project Tab, click on files from SQL Project directory
•  SQL Project Tab , right click, create new SQL Project, add new directory (uncheck use default workspace            

SYSTEM objects are filtered out  by default. 
           Change with this preference in
            "Window -> Preferences -> SQL Filtering" , Example

Objects are limited to 1000 per node (object type). 
             Change with:  Example of changing this preference

The datasource explorer caches definitions for  table, view, user etc. The definitions are used to proof read SQL and mark missing objects. If a new object has been created, outside of DB Optimizer, since it's been running, then it will be missing from the cache and flagged as non-existent in the SQL Editor. This can be fixed by refreshing the cache:

                  Window -> Preferences -> SQL Development - > Data source Indexing -> Start Indexing

                 NOTE: only objects checked in
                                            Window -> Preferences -> SQL Development - > Data source Indexing 
                           will ever be refreshed
                 NOTE: when ever DDL is run inside of DBO, the cache will be refreshed automatically to reflect any changes
                            if running DDL from some other tool, the DBO won't know to sync it's cache
        

You can  manually refresh a node in the data source explorer (for example to refresh tables only)

                    Right click on the table node in data source explorer , choose "refresh"

You can clear Data Cache to improve performance after running a long time and there is  alot of cache from multiple datasources.
                         Window -> Preferences -> SQL Development - > Data source Indexing -> Clear Index

Can only profile one data source at at time, though tuning can be run concurrently. (though you can start up a second DB Optimizer using a different workspace and profile a second data source)
Profiler .oar files are not compatible between 1.0 and 1.5. In order to read both types, 1.0 and 1.5, both versions of DBO must be installed.
Profiler .oar files can only be open with same version of database up to the two major numbers like Oracle 10.2 OAR can't be open with Oracle 10.1

                    dboptimizer.exe profile ds:<data source> duration:< minutes> tofile:<file.oar> <overwrite>
   Tune

                    dboptimizer.exe tune ds:<data source> sqlfile:<path to sql file> tofile:<tuning job save file.tun> <overwrite>

    Running command line from Performance Center

see:  Performance Center issues for command line

Enhancement Requestst
Advanced, unsupported, HSQL access