Are you having this issue on only one machine? I have Debian installed on 12 vm servers, my main laptop, and my main workstation now. I also install TDE on any machine that needs a GUI. I have never had an issue with apps accessing local storage. I use a good few IO intensive apps as well.
Something curious you said top of the line? Is this a brand new machine? You might need a more recent kernel. Personally if I have a brand new machine I use a rolling distro as Debian is a few kernel versions behind