I had the same problem at points... So...
Here is how I play chrono trigger...
I use ZSNES(PC) and PocketSNES(PocketPC).Then play it on ZSNES and save it within the game and then copy the SRM file to your PocketPC's Rom directory. You can load from your pocketpc the same way. copy the SRM file to your PC ROM directory and open it the same way. Again DO NOT USE SAVESTATES these will not work, only the actual real ingame save creates and SRM file. If you really wanna get creative. Have your Chrono rom and srm file in your sync folder. That is what I do...
I say again. SRM file not savestate files...
Should look like this.
chrono.smc
chrono.srm
chrono.zst <Savestates for ZSNES
.zs1
.zs2
P.S.
NOTICE MY SIGNATURE. I am all about CT baby!!!

__________________
GO
HERE TO SEE CHRONO TRIGGER RESURRECTION IF YOU HAVEN'T ALREADY. SQuEnix discontinued them.

Then click
HERE to sign an Online petition to allow these EXTREMELY talented people to continue this awesome remake, and to distribute as freeware.
All my themes
HERE 2...[/b]