I think the default emulator is lr-snes9x-2010.
Try installing using lr-snes9x, (latest 1.60(?)) found in optional packages.

The patch needs to be applied to a non-headered rom, though if it is working at all then it is probably the right one.

You can use 7zip to check the CRC-32.
The patched rom should have
CRC32 9C0C7C6B
And the non-headered without patch should be.
CRC32 C17ECBA5

The patch can be applied with lunar-ips. Or if the .ips patch shares the same name as the .sfc then snes9x will load the patch sidebyside without needing to change the japanese non-headered rom.

If you both patch the rom and the patch is loaded sidebyside then it might do something like you described. This only if the .ips shares the same name and is in the same folder and it has additionally been patched with lunarips.

Compatibility varies with the different versions of snes9x, there is a good chance that is all that you need.