Save as PDF with embeded images changes colors and added fog

Steps to reproduce:

open the attached file. permuted_matrices.svg
observe that the red/orange boxes have a white cross in them and are clear.
save a copy of the file in PDF format. permuted_matrices.pdf

What happened?

observe that the resulting pdf (when opened in Evince) has black crosses in the red/orange and has a foggy haze over the red/orange boxes. permuted_screenshot

What should have happened?

the pdf should look the same as the inkscape file.

Inkscape Version and Operating System:

Inkscape Version: Inkscape 0.92.3 (2405546, 2018-03-11)
Operating System: Ubuntu Linux
Operating System version: 18.10

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