Sounds like the cover may somehow be inhibiting free movement of the sail switch. The sail switch is a plate that is blown open by the fan, which closes an electrical switch. If the sail switch can't move when the fan starts, then the furnace thinks the fan isn't running and it won't light unless it knows the fan is running.
1988 Coleman Sequoia - popup (1987-2007)
2012 Roo19 - hybid (2012-2015)
2016 Mini Lite 2503S - tt (2015 - ???)
2011 Traverse LT, 3.6L, FWD
2009 Silverado Ext Cab, 5.3L, 4x4, 3.73
2016 Silverado 2500HD Dbl Cab, 6.0L 4x4, 4.10