There is no specific .Xresources to examine, so only general advice is possible.
The .Xresources file is usually loaded by xrdb (a prop for desktop settings). You can test this file by simply loading directly with xrdb, e.g.,
xrdb -merge ~/.Xresources
or just
xrdb ~/.Xresources
if you do not care for the desktop-designer's choices.
If there is some conflicting resource definition, the more specific one is used. For instance, if you had
urxvt*background: blue
and some desktop feature loads
urxvt.background: gray
you would get a gray background because the . is more specific than *.
You can see what xrdb did:
xrdb -query
If there is a resource needed by the application which is not set in the root window using xrdb, that resource is loaded according to the usual X resource rules (e.g., the system app-defaults files as well as your own .Xdefaults file).
If you are not running in a desktop environment that automatically runs xrdb, much of the advice regarding xrdb is probably not useful.
Further:
xrdb -merge ~/.Xresourcesin a file like~/.xinitrcif that file gets loaded. – joepd Feb 06 '16 at 13:55