I'm having the same problem. I have 6 mods loaded, only 2 show up.
I attached my log file and it seems that the mods are being ignored due to a missing mods.toml.
[15:42:53] [main/WARN]: Mod file Mod File: C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\grid-1.13-rift1.0.4.77-1.2.jar is missing mods.toml file
[15:42:53] [main/WARN]: File C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\grid-1.13-rift1.0.4.77-1.2.jar has been ignored - it is invalid
[15:42:53] [main/WARN]: Mod file Mod File: C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\OptiFine_1.13.2_HD_U_E6.jar is missing mods.toml file
[15:42:53] [main/WARN]: File C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\OptiFine_1.13.2_HD_U_E6.jar has been ignored - it is invalid
[15:42:53] [main/WARN]: Mod file Mod File: C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\Rift-jitpack-aeee80c1fb-1.jar is missing mods.toml file
[15:42:53] [main/WARN]: File C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\Rift-jitpack-aeee80c1fb-1.jar has been ignored - it is invalid
[15:42:53] [main/WARN]: Mod file Mod File: C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\riftmod_voxelMap_1.8.2_for_1.13.2.jar is missing mods.toml file
[15:42:53] [main/WARN]: File C:\Users\Username\AppData\Roaming\.minecraft\TGN\mods\riftmod_voxelMap_1.8.2_for_1.13.2.jar has been ignored - it is invalid
That is a really stupid reason to ignore them altogether.
latest.log