This is an issue I didn't use to have on Linux Mint but it came up after a long CafeTran hiatus. The program no longer picked up on dead keys, so for example <`> + <a> made "a" rather than "à", making it impossible to type accented characters. I found out that the reason is related to Java and ibus, which I fiddled with some time ago for use with another program.
Here is a simple solution to restore dead key functionality to CafeTran if you find yourself in a similar situation. Simply edit the 'Cafetran' bash file you use to start the program and set the XMODIFIERS variable to "", for example after this line:
cd "$progdir" XMODIFIERS=""
Restart CafeTran and it should work as expected!