Jim,
If the bore were so bad that the bullets were going downrange side ways you would definitely be able to tell by looking at it.
Any chance that your 'sometimes occurence' is the fact that two bullets holes overlap? You might try a dozen individual targets with one or two rounds apiece. They can be just plain paper or shopping bags with a black dot drawn on them.
If you still have problems I would call around to find a GOOD gunsmith and they can measure the internal diameter of the bore. Reloading fanatics do this to match there bullet sizes where they are interested in thousandths of an inch differences.
You might also try different brands of ammo. There are actually slight differences and also jacketted vs non will shoot differently. Slightly higher velocity ammo will actually cause the lead to expand just ever so much so that it fills the barrel better.
Read this post in another forum I am in to see a similar problem with a .44 cal 1892.
http://www.winchestercollector.org/forum/viewtopic.php?
t=2974
Good luck
2bit