Like DaveS said, the early 2009 11sp rear derailleurs need a modification to work with the 12/29 cassette. It's a simple replacement part (not overly expensive) that you can get. Then you're good. Newer derailleurs already have that modification done to coincide with the release of the 11sp 12/29. And there are no longer a short, med and long cage versions of the Super record derailleur. Good news is that you don't need it. Provided you have the correct chain length you should be able on run any cogset from 11/23 to 12/29, the only adjustment being a slight turning to the b-screw. I run a standard 53/39 crank and can interchange wheels using any combination of 11 spd cogs. The relevant cassettes I run are 11/23 (rarely), 12/25 (most of the time), 12/27 and 12/29.
The 10 spd versions had different cage lengths to accommodate the range if cassettes. The med cage was for the 13/29 cassette using a double chain ring up front. The long cage was to accommodate the 13/29 cassette and a triple crank up front.
Based on your experience, did switching from 12/25 to 12/29 or vice versa require adjustment of the derailleur cage screw?