After searching the forums, I found no solutiion to this issue, so I thought Id make this thread.
The issues are in the way enemies appear and the screen format.
Plugin: JabosD3D7 1.4 on Radeon 7200
Settings:
Rendering Device: D3d T&l HAL
Res: 1024x768x16
Buffer: Triple
Next 3 boxes unchecked
RSP: RSP SW 2.0X
Geo Trans: Auto
Texture format: 16 & 32
4 boxes under that are on
The issues are in the way enemies appear and the screen format.

Plugin: JabosD3D7 1.4 on Radeon 7200
Settings:
Rendering Device: D3d T&l HAL
Res: 1024x768x16
Buffer: Triple
Next 3 boxes unchecked
RSP: RSP SW 2.0X
Geo Trans: Auto
Texture format: 16 & 32
4 boxes under that are on