Can't run Mods

[wanderer1825]

I can't seem to run any mods. I've got SH4 patched to 1.4.
I've installed JSGME and Trigger Maru. Trigger Maru is in the Activated mods box.
But the game still runs the stock version.
I've tried reinstalling, different versions of TMO and still it won't work.
Any ideas?
Also, when I start the game I get the auto patch box come up every time even though it's patched to 1.4.

Tony