I just set up my Flowdock account last week. I am able to login and use the web based version but I can't get logged in using the desktop app. I'm using Windows 7 and my coworkers can get into without issue. Is there something in my account that is messed up?
I will create a case for you on this issue and one of the Support Engineers will contact you to look into it further.
A new Windows Flowdock app has been released that addresses this issue.
CA Flowdock Windows Desktop App v1.0.3 Released