OK well from first post,
Again as I said in first responce, you must have a part type defined that is actually in a library.
These warnings/erros can be cryptic, but, either one of two things you did not use the ECO process
after a first load of net list or just imported netlist and parts are really already there. Or in fact you do
not have a Part Type in your library for C1005-1608.
As far as pads outline etc not showing up but Rats Nets or connections are, under Setup/Display Colors,
you most likely have some items set to color Black or full layers turned off, but have connections set to white.
Connections will remane visible if set to a color other than black even if all parts etc are set to black
and are not visible. YOu also may have not put what you thought would be silkscreen on the right layer in Decal?
Back to first post without really seeing a netlist your libs and how you have things set up it is a litttle difficult to diagnose
but again most likely simple solutions are either parts are really already in design becuase of the way you loaded/imported netlist
and are just not visible, or you really do not have the part type in lib you really need for this Cap.