As far as I see you're trying to make two simultaneous connections to the public streaming endpoints (a.k.a. general streams or stream.twitter.com) from the same IP.
More specifically, I think you want two active connections to stream.twitter.com/1.1/statuses/filter.json from the same IP.
Although the Twitter streaming-apis documentation doesn't clearly say about only one standing connection to the public endpoints, the Twitter employees clarify this on the dev site https://dev.twitter.com/discussions/7542
For general streams, you should only make one connection from the same IP.
This means that it doesn't matter you use two different Twitter applications/accounts to connect to public streams; as long you're connecting from the same IP address you can have only one standing connection to the public streams. You said that you got both streams connected, and the answer to this behaviour is given by a Twitter employee: https://dev.twitter.com/discussions/14935
You may find that at times stream.twitter.com lets you get away with more open connections here or there, but that behavior shouldn't be counted on.
If you try for instance, in the 2nd thread, to connect to user stream instead (twitter4j TwitterStream user() method), then you'll really start getting both filter & user streams.
Regarding the 200 track keywords limit, probably the twitter4j.org javadoc is little bit outdated. Here is what the twitter api docs are saying
The default access level allows up to 400 track keywords, 5,000 follow userids and 25 0.1-360 degree location boxes. If you need elevated access to the Streaming API, you should explore our partner providers of Twitter data ...
So, if you need to go beyond the 400, you'll probably want to ask Twitter for increased track access level for your Twitter account application, or working with certified partner providers of Twitter data.
Another thing you don't necessarily need, is starting new threads for getting the streams, since the twitter4j filter (or user) "method internally creates a thread which manipulates TwitterStream and calls adequate listener methods continuously" (quoted from an example code by Yusuke Yamamoto).
I hope this help. (I couldn't post more links because I'm getting this "You need at least 10 reputation to post more than 2 links")