It's very possible, even likely, that middle chainring-small cog is just a combination that shouldn't be used. Putting the chain on the outside rear cog results in a severe chain angle that sometimes simply can't avoid having the chain hit the large chainring. It will depend on chainstay length and lateral spacing of the cogs and chainrings and the size of the chainrings whether this gear is usable or not.
Shimano chainrings have ramps and pins built into the inner surface of the large chainring. That may be what is catching your chain. It's built that way to make shifting easier. To check if the chainring might be bent, drop the chain to the inside and eyeball the teeth from above as you turn the crankset. You can hold something like a large screwdriver so it just touches the teeth while you turn to see if they are all aligned.
Oil is good, grease is better.
2007 Peter Mooney w/S&S couplers/Terry Butterfly
1993 Bridgestone MB-3/Avocet O2 Air 40W
1980 Columbus Frame with 1970 Campy parts
1954 Raleigh 3-speed/Brooks B72