I suggest you use the official builds while troubleshooting the issue, so you're not limited to receiving support in the Ishiiruka thread.
Did it use to work with a previous version? If so, could you try to bisect? (find the first broken Dolphin version with this issue)
I cannot reproduce this with the latest version of the texture pack, with a fairly up-to-date version of Dolphin, the OpenGL backend (on Linux) using the OoT Master Quest game.
edit: FYI, if something doesn't work in the master (i.e., official development) builds, it's unlikely to work in Ishiiruka since those are based on master. And Ishiiruka could even introduce more problems and its own issues.
Did it use to work with a previous version? If so, could you try to bisect? (find the first broken Dolphin version with this issue)
I cannot reproduce this with the latest version of the texture pack, with a fairly up-to-date version of Dolphin, the OpenGL backend (on Linux) using the OoT Master Quest game.
edit: FYI, if something doesn't work in the master (i.e., official development) builds, it's unlikely to work in Ishiiruka since those are based on master. And Ishiiruka could even introduce more problems and its own issues.