Same here... (PBI Server Version 1.1.6582.41691 (October 2017))
I got 2 tables as a web source and I need to merge them into 1 table.
These tables have already different column names but I tried to rename them in the merged table to make sure they are unique in Power Bi Desktop.
Manual refresh works fine... but scheduled refresh on Server doesn't work...
Hope someone has a workaround for this situation too
I can confirm the same issue on my end, with the added twist that I had a report working with a data refresh until I added a Merge Queries action. I have resolved the situation using the stated workaround of making sure both queries involved in the merge action are sourced from a table rather than a SQL query.
In my specific case, I had a SQL view-based fact table with a column named "FiscalYear" imported using a SQL query that was filtering on a separate SQL view containing a limited number of fiscal years. I also had a dimension table for the fiscal years using a table data source from the same view containing a limited number of fiscal years.
I then decided to limit the report to the current FY plus the prior 10, which required implementing the Merged Queries action on the fact table and a Keep First Rows action on the fiscal years dimension. The data refreshed fine in PBIRS Desktop (October 2017), but the scheduled refresh under PBIRS failed.
For the workaround, I modified the data source for the fact table to pull directly from the view with no SQL query filtering in Power BI. As soon as I did that, the Desktop refresh worked and running the scheduled refresh on the server also worked.
I hope this info helps identify the issue. I am looking forward to the next release of PBIRS!