Product:
Cognos Controller 10.4
https://www-01.ibm.com/support/docview.wss?uid=ibm10735239
Microsoft Windows 2016 Server

Problem:
After upgrade to a later version of Cognos Controller 10.4, where also BI 10 have been replaced by CA11, the PDF shown inside Cognos Controller client is small. HTML reports works fine.

Solution:
The user profile of the user executing the report is referencing a style (also known as skin) from IBM Cognos Business Intelligence 10.

In IBM® Cognos® Analytics, in the lower-left corner, click icon for administration, select Administration Console.
On the Security tab, click Users, Groups, and Roles.
Click the namespace that contains the user.
Find the user whose preferences you want to view or change. You can use the Search feature to find a user Searching for entries using name, description, and name or description.
For that user – in the Actions column, click More.
Click Set preferences.
Click the different tabs to view or change the settings.
In the Preferences tab, choose Style Corporate.
Make the change and click OK.

Test again to run a report in Cognos Controller as PDF.

More Information:
https://www-01.ibm.com/support/docview.wss?uid=ibm10739581
https://www.ibm.com/support/knowledgecenter/SSEP7J_11.0.0/com.ibm.swg.ba.cognos.ug_cra.doc/t_viewchange_userprofile.html