So far, you've not listed an application from the MATE desktop as being
affected by this issue, in fact you specifically state that Caja (the
MATE file manager) work correctly.
I also have no way to reproduce this issue given your exotic hardware
configuration :-(
** Also affects: dolphin (Ubuntu)
Importance: Undecided
Status: New
** Also affects: vlc (Ubuntu)
Importance: Undecided
Status: New
** Changed in: ubuntu-mate
Status: New => Invalid
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Bugs, which is subscribed to dolphin in Ubuntu.
https://bugs.launchpad.net/bugs/1637034
Title:
Ubuntu Mate 16.04 mouse inputs not handled correctly on multi gpu
system
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https://bugs.launchpad.net/ubuntu-mate/+bug/1637034/+subscriptions
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