(Legitimate) Pop up Windows every time Firefox starts

So, lately each time I fire up Firefox, the new browsing session recovers pop up windows from previous sessions (from the last time or even some from like, three days ago) I have long closed down. My start up option has always been "Show my windows and tabs from last time" which used to do exactly that: recover tabs I had opened or start with a new blank tab in case I had none opened. Now though, each time I open FIrefox I am getting various windows from previous session(s).
The catch here is that this doesn't APPEAR to be a malware issue since I am not getting weird ad/dodgy windows but "legitimate" pop ups I remember I have personally triggered i.e a picture or frame from a trusted site which opened into a new window or a help section from amazon.com etc.
This is a first and as you can imagine it has become really annoying. I am using Firefox 25.0.1.
Any ideas? Thanks!

Thanks for your replies philipp and james
Yeah, it seems it's a case of firefox not shutting down properly since the problem appeared ever since I've begun closing down firefox by ending the process (mind you, with a cmd shortcut icon even) in an attempt to efficiently escape from the never-ending flash player script hangs/crashes (disabling hardware acceleration or reinstalling flash player doesn't help).
Deleting all the sessionstore ... files solved the pop up windows issue.

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