I am looking for a roadbike. I am about 5'6 1/2". On Trek bikes I am a 52. The sizing on Giant though is S/M/L. I road a Giant Avail Comp 1 in medium and it was very painful on my arms. They were very over extended. Today I road an avail comp 2 in small and had no issues with my arms. Is a small the right size? The LBS today said I was a small not a medium. The other LBS said the opposite. I can't find online on the giant site what the sizes are equivalent to....

Giant Road Bike » Bike Fitting Charts
You are on the edge of a small and a medium. I suggest you ride both and pick the one that feels right to you. The sizing charts are for general sizing anyhow, it gives you a place to start.

At 5'6" that would put you at S on Giant's sizing chart. I've recommended several people with the same height as you the same and they have no complaints riding the bike.

The arm pain is due to overexertion from a very long top tube + stem.

It's easier to fix reach on a smaller bike using a longer stem.

Stay away from the LBS that is selling you the medium. They probably just want to dispose of the M sized bike.

I know what you mean. I am 5 ' 4 1/2" and a giant avail small was too long a reach where an xs was too compact. On Trek the 52 was good and even the 54 felt comfortable. After trying several I am going with a 51 Cannondale (on layaway). I wish sizing were more universal between companies. But then I suppose it is nice to have many fits for finding just the right bike

You are quite likely a Giant S. I have ridden large 54 cm bikes (c-c in steel, so very much like a 55-56 cm when measured c-t) for over 30 years and fit quite nicely on a Giant M. Your preference for 52 cm bikes suggests you should focus on the Giant S.

Take the frame manufacturer's sizes just for a ballpark figure. Most manufacturers still use the outdated method of using the seat tube length as the frame size, which has nothing to do with handlebar reach.

Experienced cyclists look more at the horizontal top tube length and frame reach to determine similar frame sizes, and ultimately fit, between manufacturers.

I am 5'7" and the Defy in a Medium is perfect. My torso is longer in proportion to my legs. I tried a small and it was too small.