It is great that you got it to work with vcd2saif.
However, that should not be necessary. I suspect you need to use the -vcd_scope (or -vcd_module in older releases) option to read_vcd in order to select the "scope" in the VCD that you want to apply to the top design in RC.
It is very common for a VCD to only contain signals from the design you are interested in, but also contain the full hierarchy from the testbench. For example, your VCD may look like this:
$scope module tb $end
$scope module dut $end
$scope module my_top_design $end
$var wire 1 Tc4# clk $end
$var wire 1 Eb4# reset_n $end
In this above case, you need to specify "read_vcd -vcd_scope tb/dut/my_top_design ..." or just "read_vcd -vcd_scope my_top_design ...".