The solution turned out to be windows cmd: "tree /F /A > my_out.txt" and some Python.

C:\Users\Evan\Documents\temp\adobe_workdir>python
Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> def produceDict(filename):
...     currQueue = "null"
...     k= 0
...     res = {}
...     for line in open(filename):
...             if line[0] == "+":
...                     res[currQueue]=k
...                     k=0
...                     currQueue = line
...             else:
...                     k+=1
...     return res
...
>>> rDict = produceDict("ryan_out.txt")
>>> eDict = produceDict("my_out.txt")
>>> for key in rDict:
...     try:
...             if rDict[key] != eDict[key]: print key
...     except:
...             print "ERROR"
...             print key
...
+---AdobeDreamweaver11-mul

+---AdobeContribute6-mul

ERROR
+---TLF_Flash11-mul

+---AdobeFontsRecommended-mul

+---AdobeIllustrator15-mul

The problem was 6 missing files in a 7GB download off a VPN server that takes a minute to display each of the 165 possible folders from which files might be missing. More fault of my Internet though. (Sadly, Adobe took the CS5 downloads down.)