I've had to quit using Cookie 5.0.3.8.8, as it is spiking CPU usage to 140% or so. 
MacBook cycles from 0% to 140%, iMac remains steady at around 130%.
"App busy" spinning graphic appears in Cookie window. 
But it's not frozen, as I can still delete tracking cookies in this state.

El Capitan 10.11.4,  Cookie beta 5.0.3.8.8, running current Firefox and Safari

Thanks, the beta appears to have worked, cruising along on both machines fine today, no more access popups.
Cheers.

I have the same issue. "cookie needs to access this path to continue" dialog box pops up after startup asking for access to Macromedia folder, have to click 'OK' 17 times or so to resolve, Cancel does not stick. Allowing computer to sit for several minutes usually resolves it on its own. Issue occurs with same user on two different Macs. Has been happening for a few weeks now.

Cookie 5.0.3, Mac OSX 10.11.4