In general you don't care 2 different things that way, and it depends on
several other thing's beside the brightness.

- 85mm vs 50mm have 2 different set of leneses (requirement)

- If you capture the same subject then the 85mm should be 35mm closer, the
subject should be around 1/3 closer (larger), so the subject should be
brighter (this many people don't pay much attention to)

    Same with the very same ZOOM lens, you can get the same subject larger,
brighter, sharper by zoom in closer.  Or this is one of the tricks or
advance of long zoom lens when shooting in low-light situation.

- Also, you can look at the very end of the lens (the part attachs to the
body) and you may see some difference there (or I don't have yours to
confirm but I know some do have the size difference, and when talking about
size I also mean LIGHT).

I doubt that you actually have a problem, if for no
other reason than a full fstop difference is a very
significant amount of light reduction (from scratches,
fungus, misadjustment, etc), and you would almost
certainly be able to see *anything* that would cause
such a huge variation.

Regardless of that, I have a 50mm f/1.8 and also an 85mm
f/1.8, so it was rather easy for me to check mine for a
variation.  I'd expect though, that you will be
interested in just how I checked, because you will need
to do something similar to determine if your lenses are
actually different.

I set up a test scene.  I pinned an "Eskimo mask", that
is about 10 inches in diameter to an off-white colored
cardboard box, and used a single light from about 5 to 6
feet away directly behind and above the camera (a D2x on
a tripod).  Neither the box nor the mask showed any
reflections.  The area of the mask is perhaps 15% black
and it has no white areas.  (The face is a tan color,
which with a spot meter measured at the same reading as
the entire scene did when the 85mm lense was used.)

The camera to object distance was adjusted with the 85mm
lense in place for a full frame top to bottom image,
which left some white off to the sides.  When the 85mm
lense was replaced with the 50mm lense the angle of view
changed, and a larger area of white background was
framed than had been true with the 85mm lense.

The camera initially was set for full frame metering,
and shutter priority was selected.  The shutter speed
was at 1/10th of a second for all images.  With the 50mm
lense it metered at f/11, and with the 85mm lense it
metered at f/10.  (The camera was set for 1/3 fstop
steps, so this is less than the difference you reported,
but is not insignificant.)

I then set the camera to manual mode, and used the
blink-on-overexposure LCD display as an aid in setting
the aperture.  With either lense there was no blinking
at f/6.3, and there was at least some blinking at f/5.6.

There are several conclusions which can be reached from the
above:

 1)  The *correct* exposure was at f/6.3.

 2)  The light tranmission of these two lenses differs
     by less than 2/3 of an fstop.

 3)  Full screen metering is very easy to fool.

      A)  The overall brightness of the scene was
          greater than 18% gray.

      B)  The 85mm lense's field of view allowed
          enough of the white background to be part
          of the scene to skew the measurement by
          1-1/3 fstop.

      C)  The 50mm lense's field of view allowed
          enough of te white background to be part
          of the scen to skew the measurement by
          1-2/3 fstop.