IS300 allingment issues

I was hit on the driver side by a car changing lanes who forgot there
might be other cars on the road. We were not traveling fast, and I was
able to avoid most damage. Only the fender was dinged and needed
repairs. Insurance took its time to get settled, and when that finally
happened I took the car in to be repaired. I drove the car for about 2
weeks before repairs and over that time there was no change in
drivability or handling.
Now the car is almost finished but the repair shop has encountered a
problem. Apparently the car is 3 degrees out of alignment. From what
I know about alignment 3 degrees is a lot, probably easily visible just
by looking. I went over the the shop, they had the car on a lift, and
with the shop manager we measured several points along the control arm
and u-joint to points on the frame. Everything came back identical to
the other side. There is nothing we can see that is wrong, but the
computer still spits out the 3 degree off reading. We even did it on
another machine to test it out.
Now they want to throw some parts at the front end to see if that will
solve the problem. The only problem is the car is driving perfectly,
with no pulling or miss aligned steering.
Does anyone out there know of another problem that might be causing
this alignment error? The shop seems pretty well run so I don't think
they are trying to pull anything over on me, and insurance is paying
anyway. But they still can't really tell me what is wrong. Any ideas?

3 degrees? Since you seem genuinely interested in knowing....

A car's front wheels have several alignment adjustments: camber, caster
and toe-in.

Camber is each wheel's vertical angle which is expressed as degrees from
90 degrees meaning that the wheel is 90 degrees vertical to the roadway
(usually) plus about 1/4 or 1/2 of one degree so the top of the wheel is
ever so slightly farther out from the axle than the wheel's bottom. To
much or too little camber causes tread wear on one or the other side of
the tread and can also cause a car to "pull" to one side.

Caster is the angle between the wheel's top and bottom pivot points, its
also known as the kingpin angle (even though cars haven't used king pins
since the '50s). I believe this is what's 3 degrees "off" not something
that can be measured with a tape for the angle only shows itself when
the front wheels are turned, not straight ahead. The effect of this
angle is felt in a car's steering as under or oversteer, also called
"wandering" - it won't stay straight, even on a straight and flat road.
One enters a turn at say 50 mph and the car is slow to respond so one
turns a bit more and suddenly the car oversteers and turns too sharply.
One may notice 3 degrees or not. Caster doesn't much affect tread wear.

Toe-in is the front tires' parallelism. The wheels should be slightly
closer (1/8 to 1/4 inch) at their leading edges vs. their trailing
edges. The tires' rolling resistance "presses" the steering linkage and
the toe-in is absorbed by the slight looseness in the linkage allowing
the wheels to be parallel.

Body shops check alignment and insurance companies pay for that to avoid
liability of releasing a repaired but unsafe car to its owner. I suspect
that your car may have had the 3 degree caster difference between its
left and right sides before the incident; if not, then the incident bent
the car's structure - unlikely given your description.

Hope this helps you get back on the road.