I know that there were some issues with BA in Dynamics GP 2016 R2 that were fixed in later versions.
Even with default SSRS reports, I know I had a case with a similar issue and in my testing, with BA in GP 2016, I added 3 reports to be shown in BA, but it would only show 2 of the 3 reports at all.
To further test, I added a total of 10 reports to BA in GP 2016, again, even after refreshing, only 2 of the reports shown.
However, in GP 18.3, I added 8 SSRS reports to show in BA in testing, and I can view and look at all 8 in the BA section of the Home page.
Based on this, it does appear there is an issue with BA section of the GP Home page in Dynamics GP 2016 R2 that was fixed in later versions.
My recommendation would be to access these custom SSRS reports via the 'Reporting Services Reports' links on the area pages in GP 2016 R2, until the client upgrades to Dynamics GP 18.3 or so.
Thanks,