I tried The Legend of Zelda: Spirit Tracks (USA) with the D-Pad patch, I have no issues with the CPad patch (both the analog movement and the L + R + Down combination work); I am on a New 3DS with Luma3DS v13.0.2, TWiLightMenu v26.7.0 + nds-bootstrap v1.3.2, and TWPatch at 2023/07/22 build.
The CRC32 of the clean USA ROM for the D-Pad patch is 3170189F, and the GameID of the D-Pad patched ROM is BKIE-5818C636, check that yours match with these.
And be sure that the cheat of the CPad patch is active, obviously.