I was receiving an error whenever I was trying to run a stored process through the add-in found in custom repository. A technical support post http://support.sas.com/techsup/unotes/SN/019/019110.html
explained that the problem I was having is caused by duplicate folder names between the foundation and custom repository. After I altered the names of the folders I was able to run stored process found within a custom repository.
However there is still one issue with this work around. The difficulty with this requrirement is that when a new repository is created the BIP Tree folder is created automatically. You have to delete it in order for AMO to run properly. Once the BIP Tree folder is removed then any reports in the custom repository can not be run through Web Report Studio. What is the best way to circumvent the problem with duplicate folder names but still allow for the stored processes in a custom repository to be run in BI Tools other than the Add-In?
That's a good question without a good answer today. We are working on some larger changes that remove this issue, but the next release is still a good way out. So, while there's no good answer today, we are working on the problem and a solution is coming!