Hi.
Make sure your clones are unlinked - select all objects and unlink - ( Shift-Ctrl-D )
Tried to make some tiled clones and got no problems filling the colors using the dropper tool.
Be aware that you can copy ( CTRL - C ) and paste the stroke and fill only by - ( Shift-Ctrl-V )
When copying gradients the gradient does not show until "activated" by clicking
the gradient icon on the toolbar - strange, you might have the same problems with patterns.
The color fill for the hearts was picked from the rectangles.
Last row of hearts was cloned manually and gradients & filters applied by the dropper tool.

Click image for larger version.
Good Luck.
RGDS
Ragnar