Actually, the internal tuner can effect the readeings.  If you want an 
accurate reading, be sure the tuner is off.  The tuner makes the radio see 
50 ohms, but the impedence of the line and load on the output, the 
antenna, and the load back toward the radio, the tuner, can be far from 50 
ohms.  The meter is designed to run in a 50 ohm circuit, which it isn't 
any more.  I fought this battle a while back trying to tune up a six meter 
antenna on the 2000, and got all kinds of strange readings until I 
remembered to turn off the tuner.  The tuner does effect things, because 
it can present a high impedence to the meter on that end.  Also, you'll 
find that sometimes just changing the length of the cable between the rig 
and the meter can change readings.  I had a regincy 2 meter rig once and I 
was just a beginner in all this stuff.  I had run another radio on my 2 
meter beam and knew the beam was working great.  The regincy worked great 
on my mobile, but when I hooked it up to the beam, no output.  As they 
came from regincy, they were very sensative to a "high s w r", and would 
shut down.  I thought o.k., I'll check the swr.  Put the meter in the 
line, and radio worked fine.  Took the meter out, and no output.  I 
finally found that by either adding 6 inches or cutting six inches off of 
the line made the thing work.  It was dependant on exactly where in this 
run of 70 feet of coax the radio was.
This is why if you are checking the s w r on a 72 ohm line, you have to 
change some resisters in the meter so it matches the line.
73s
Butch Bussen
wa0vjr