Both return the same Session Id (a Visualforce Session Id). I seem to recall that other users have had trouble in the past trying to launch Conga from Skuid with Conga’s Report-driven document merge approach, as opposed to the Conga Queries document merge approach. The reason is that the Report-driven approach requires a “Salesforce” Session Id, as opposed to a Visualforce Session Id. Because Skuid runs in Visualforce, Skuid gets a Visualforce Session Id, which seems to work for Conga Queries / SOQL-query based merges. 

I searched the Community to try to find an example of someone succeeding with a Report-based Conga query launched from Skuid, but haven’t found one yet.

Zach, thank you for the response.  Is there an API to call a SF button via Javascript? 

For this:

Peter, will the button included on the Skuid Page? If so, you could give the Button a Unique Id and then trigger a click on it via JavaScript, e.g. via

skuid.$(‘#MyButton’).click();
or 
skuid.$(‘#MyButton’).trigger(‘click’);

If you don’t want the button to be included on the Skuid Page at all, then no, there’s currently not a documented Skuid API for doing this, but we could potentially add that if it was a significant need.

Thanks!  As an FYI here is how I solved this issue… feels pretty hacky but it works!

var partnerServerExternal = sforce&#46;connection&#46;partnerServerUrlsr24];<br />var partnerServer = partnerServerExternal&#46;replace("mycompany--skuid&#46;na1&#46;visual&#46;force&#46;com","mycompany&#46;my&#46;salesforce&#46;com");<br />&nbsp; &nbsp;&nbsp;<br />&nbsp; &nbsp; var URL = '<a href="https://www.appextremes.com/apps/conga/pm.aspx&#39;+" rel="nofollow" target="_blank" title="Link https//wwwappextremescom/apps/conga/pmaspx">https:&#47;&#47;www&#46;appextremes&#46;com/apps/conga/pm&#46;aspx'+</a>&nbsp;<br />&nbsp; &nbsp; &nbsp; &nbsp; '?sessionId='+sforce&#46;connection&#46;sessionId+<br />&nbsp; &nbsp; &nbsp; &nbsp; '&amp;serverUrl='+partnerServer+&#46;&#46;&#46;

Interesting! So you used the same Session Id, you just used a Server URL on the *.salesforce.com Domain tree, rather than on the *.force.com tree, and it worked — that is very helpful. Good to know.