I think you did the right thing. Engines will take a while until they re-crawl your robots.txt and actually following what you commanded.

Extra steps I would take:

• 302 the redirect, probably is just a line of code doing the redirect after setting some cookies or session variables.
• Try to edit the affiliate codes to work with Javascript instead of naked URLs ( could be something like <ins class="affiliate">that is later switched to a text link or banner using JS). This will not only allow you to set a nofollow for those links, but you could be able to remove/block specific affiliates or pages where you don't want your links/banners.</ins>
  

PS: have you tried fetching your robots.txt from Google WT (Crawl -> Blocked URLs) to see when was it downloaded and id the contents are ok?

But did you get any MANUAL penalty on A or B?

Hey Chris,

Did site A or B receive a manual penalty?

As any penalty on A, which is 301'd to B, will ultimately pass the penalty to B. I would suggest removing the 301 ASAP. Then cleanup the A domain until it's clean (if a manual action, until it's revoked) and then you can think of putting the 301 back.

Removing a manual penalty could be a long process, it took 1 year for us and 4 reconsideration requests to get the penalty revoked. We had to use the disavow as a machete as disavowed almost our entire link profile leaving aside the domains that we knew were good links, all others were disavowed using the "Domain:" to avoid any missed link.