I've not seen the boot catch on an FD2 yet but I have had quite a lot of experience with other Japanese cars, namely Subaru's so this might be a similar set up.
If you open the boot with the remote then have a look at the boot catch, see if there is a small lever on it or near by, similar to a child lock, it's possible you might have accidently flicked it to the locked position. All this does is stop the manual boot release working, i assume to try and make it harder for someone to get into your boot should they break a window.
Cheers
Kenny