When I try to run the 3D test in the DXDIAG program for both of the cards, I get these messages:

Ti4400
Direct3D 7 test results: Failure at step 8 (Creating 3D Device): HRESULT = 0x887602eb (error code)
Direct3D 8 test results: Failure at step 8 (Creating 3D Device): HRESULT = 0x8876086a (3D not available)
Direct3D 9 test results: Failure at step 8 (Creating 3D Device): HRESULT = 0x8876086a (3D not available)

VooDoo2
Direct3D 7 test results: Failure at step 46 (GetDC): HRESULT = 0x88760249 (Can't create DC)
Direct3D 8 test results: Failure at step 8 (Creating 3D Device): HRESULT = 0x8876086a (3D not available)

I uninstalled DirectX using DirectX Buster and re-installed the DX9c version as some games require DX9c in order to get it working. My plan is to uninstall DirectX again and install DX8 from the game Jimmy Neutron Boy Genius and see if that fixes it. It's not a driver error and I already reinstalled the drivers for the Ti4400 card. And the nVidia software reports the cars is running on AGP 2x over AGP 4x (the BIOS is set to AGP 4x). Running the Windows 98SE installation to write over the files and see what happens.

What could be the issue? And if this is in the wrong spot, feel free to move this.

I reinstalled Windows 98SE by booting from the CD and it still won't work. After installing DirectX 8, my VooDoo2 card was working fine. After installing DirectX 9b, everything went south again.

After further diagnostics, I installed the VIA chipset drivers for both the board itself and the AGP slot. I also did some more further testing and DXDIAG shows the full 128MB RAM on my Ti4400 AGP, but the nVidia Display Control Panel shows that it's running on AGP 2X over AGP 4X. I ran the test for both cards and the Direct3D didn't show any errors on the Ti4400 AGP card (success), but the VooDoo2 card still has an error message:

Direct3D 7 test results: Failure at step 46 (GetDC): HRESULT = 0x88760249 (Can't create DC)
Direct3D 8 test results: All tests were successful.
Direct3D 9 test results: Display driver does not support API (DDI version too low) --> normal message as the VooDoo2 card only supports DX7-8 anyway.

Ti4400 AGP results:
Direct3D 7 test results: All tests were successful.
Direct3D 8 test results: All tests were successful.
Direct3D 9 test results: All tests were successful.

Getting a bit closer for the VooDoo2 card and I think it's because I forgot to reset the system after installing the FastVooDoo 4.6 drivers again.