Now only in status bar and no more popup window. Previously, it only showed once until a restart, but now it shows every time it detects a new version online. Since it does not show a popup window it's not a big deal.
PyBitmessage
Bitmessage is a P2P communications protocol used to send encrypted messages to another person or to many subscribers. It is decentralized and trustless, meaning that you need-not inherently trust any entities like root certificate authorities. It uses strong authentication, which means that the sender of a message cannot be spoofed, and it aims to hide "non-content" data, like the sender and receiver of messages, from passive eavesdroppers like those running warrantless wiretapping programs.
Development
Bitmessage is a collaborative project. You are welcome to submit pull requests although if you plan to put a non-trivial amount of work into coding new features, it is recommended that you first solicit feedback on the DevTalk pseudo-mailing list: BM-2D9QKN4teYRvoq2fyzpiftPh9WP9qggtzh