Sorry my friend, but this is problem of Sparky, not Clementine.
In Manjaro, Mint 18 and Mint Debian Edition, Ape files are working properly.
I tried many of other distros, and I never saw something like this. Ape files are working, or they are not working at all.
This is the middle variant.
PS I tried other players like Deadbeef, but equalizers are problem. I tried Audacious, but I have problem with adding of folders.