Thomas,

The Selection of Vref is in ADCON1 as you said, make sure you are
setting it to xxxxx001 to have RA3 as Vref.  Setting ADCON1 to all
zeroes is the reset default, where Vcc is the ref.  Is it possible
you're getting an unintended reset which trashes the ADCON1?

The data sheet does not allow a Vref below 3V.  Its in the A/D
converter section, DC characteristics.  (Parameter A20).  Vref range
is allowed to be 3V to Vdd+0.3, (I assume the upper limit is where
the over-voltage protection diodes on RA3 begin to turn on.)  That
said, I am using mine with 2.55V reference (10 mV per count), and
seems to be working fine.  I asked the FAE why the 3V min, and it
comes down to the allowable offset in the comparator that is the
heart of the A/D.  If Vref is smaller than the 3V spec, the
comparator error budget is << 10 mV.  So a "good" one should work
fine at 2.50V Vref.  I don't think that is your problem.

-Barry.
------------
Barry King, KA1NLH
NRG Systems "Measuring the Wind's Energy"
http://www.nrgsystems.com
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