That picture looks like it is most likely a .ips compatibility issue. Did you make any manual adjustments to your ROM or the bundled .ips file? Since Mesen auto-patches the bundled .ips file, no manual adjustments should be necessary. I have heard that some individuals tried to manually patch before using the pack and it caused the issue in your picture. Also, does your ROM match the requirements noted near the download section? The pack must be used with a USA Zelda ROM (PRG0) that has a SHA-1 checksum of DAB79C84934F9AA5DB4E7DAD390E5D0C12443FA2. Otherwise, it will likely have issues like the problem shown in the picture.
I think you called it. It was a combination of the ROM version as well as a tutorial I found on Youtube that said to remove the alternate folders in the remastered folder within the HDPacks. It's working great now. Thanks for the quick response.