Multiple Twitter Accounts - Are their logins conflicting with other web apps?

I have been using two web apps that have multiple twitter accounts in their interfaces: Threadsy and CoTweet.

The problem being that if I go to Retweet something or tweet a URI via Bitly or a similar action on the web, it will choose one of the accounts that I am not actually logged into via Twitter.com or via Bitly.

I don't use desktop apps, only web based and will stay logged into my Primary Twitter account all day via Twitter.com or Bitly.

CoTweet swear that it is not their web app that is conflicting with the signed in twitter account.

Maybe you can check this out, but I have now removed all but my primary twitter account from Threadsy and will monitor the situation.

I use Google Chrome and not sure if it's a cookie type issue.