I've just noticed this problem recently where I'll get strange sounds/pops when I bounce offline. It has happened in multiple projects, so it's hard to imagine it's a plugin issue.
I've tried disabling normalization (I usually only use it for overload protection anyways).
When I bounce in realtime it usually removes the issue. I suppose I could do that, it's just annoying not to be able to offline bounce anymore.
Currently on OS 10.10.5
I don't think it's plugin related but here are some common ones I run. Izotope RX, Omnisphere, Space Designer
Any ideas would be helpful.