I'm not entirely sure why FlashFXP so slow for you, That is not the normal behavior. From start up to interface should be around 0-10 seconds at the most. maybe a little slower on older hardware or but still very responsive.
The same goes for changing directories, A change should be instant unless maybe there are thousands of files in the folder and then it might take a bit longer. One thing you can do to determine if the local view is also slowing down the start up is to toggle the local view to ftp view by clicking the right most button on the toolbar for that side. Exit and restart FlashFXP
Another thing we can test is maybe a 3rd party application is causing the slow down. You've ruled out anti-virus and firewall but maybe it's something more obscure. You can try unchecking "Accurate file system shell icons" located in Options > Preferences > Display > Options. When this option is unchecked the local view is a bit faster because it doesn't have to query each file for it's own icon, it uses the file extension default.
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