Hmm... well first, welcome. Secondly, here's what I would suggest you do to get it to work.
1. Make sure you're using the unheadered patch. I guess the headered one will mess with the ROM.
2. Make sure you're using a clean ROM. Make a copy of your standard Chrono Trigger ROM with no patches on it and patch the PG patch to it. You don't mix patches. Kind of like you don't mix heroin and booze.
3. Make sure it's a good ROM, as well. I've read tales of the ROM going kind of boom because someone did something bad to the ROM.
4. Get the latest version of your emulator. It might not be able to read it for some reason.
5. Give it a little bit. It may take a little bit for your computer to get what's going on. Especially if your computer is old.
6. If all else fails, poke it. This has helped me quite a bit.
Let me know if any of this helps, 'kay?