1/ Do you have other Settings that Analysis for Office will automatically be opened?
I think this depends on the load behavior of the Analysis Add-In. If you would check the Admin Guide for A4O (easily found in help.sap.com), paragraph 5.3 you see the different options.
My shortcut looks as follows: <<<"C:\Program Files (x86)\SAP BusinessObjects\Office AddIn\BiOfficeLauncher.exe" /app XLS /lb 3>>> where the /lb 3 means it is enabled when you start Excel. I think it basically comes down to once starting the A4E via this shortcut. If you then in the future start Excel in any other way, the add-in will already be enabled (which is the difference with "/lb 13 i think)
2/ Do you use IOMS
We actually don't use sharepoint as a portal for Analysis for Office, so i have no idea what IOMS is :-). I just wanted to test your scenario as it sounded interesting (since we are rolling out Analysis in the near future and have an underused sharepoint portal...)