1995 Jaguar convertable XJS quarter light windows wont go up

The rear windows are controlled by a timer in the top's ECU. If
the rear windows stop fully closing before your top is closed, the
problem MAY be with top's hydraulic system.

Check your top's hydraulic reserve tank for low fluid level. Lack
of fluid will greatly delay the top's closing sequence, leaving
those rear windows partially open.
Your top's hydraulic pump system is located beneath the right side
of the cubby/storage box behind the front seats. Raise the cover
and you'll see a removable trim panel on the right side. The pump
is behind that access panel.

You can use power steering fluid to top off the tank, but don't
fill it above level indicator line. You may have to add more fluid
after you cycle the top up and down to get the air bubbles out of
the lines.
It could also be a relay. On a 95 the relays that are in the trunk above the battery.
Perhaps, just switching the relays might prove which one is failing..