This bug is resolver in Qlik NPrinting 126.96.36.199. From the release notes:
Reports based on Excel templates ignore custom row heights
In Excel templates, row heights set in template editor with the Keep Source Formats check box unflagged were ignored. Row heights changed in the template file are now kept in the output report.
So, if you can, upgrade to Qlik NPrinting 188.8.131.52 and check if this resolves. You can test this bug fix also on a development computer.