Are you using tremake correctly? I'm not sure if it would crash otherwise, but it's something to check I suppose...
You have to use it to make a whole folder, with subfolders, into a TRE file. For example, you have to take all the folders that contain your modified files (ie: \mission, \mesh, etc) and put them inside a "mymod" folder... and place that "mymod" folder inside the folder tremake is in. Then you run "tremake mymod.tre mymod"... it takes all the stuff inside "mymod" and makes a TRE from it (while keeping the files' additional path info... so whatever was in \mymod\mission will be saved in the TRE's \mission, etc).