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I would also like to add that running the msi for the client in any mode other than full resulted in the msi not installing at all(it would start installing then die off). When I looked into the msi I came across numerous custom actions that were not set to ignore the error code, thus these are what caused it to stop installing. All I did at the end of the day was repackage it. You'll also have to include the temporary folder and files it creates when it is launched by another client(say Cognos). These files and folders are created under c:\Program Files\IBM\SQLLIB\DB2.
The issue noted above isn't so much that the CAs check for a return code, rather it's that the UI sequence contains CAs which don't appear in EI at all (and vice-versa). I'll try and remember to post the list once I've completed my transform.