I have a similar issue. 3GS on 4.0 JB via pwnage. It worked great until I installed mywi. It will see the router, one at home, one at work. At first it wouldn't connect at all. Tried forgetting the networks and that didn't help. Long story short, I finally got it to connect by putting it in airplane mode, waiting for it to connect than disabling airplane mode. After that I kept having to go into settings and manually select the router. Not a big deal. Well, if I put it to sleep it wouldn't rejoin. Now, out of nowhere, it decides to auto join. For the record, the work one never gave me any issues.