This is a weird problem. On my 1991 Civic the Rubber boot on the CV joint - right where it goes into the trans- is rubbing aginst the bottom of the engine and tearing the boot. I put in new motor mounts- thinking that after 15 years the rubber may be deteriorating and sagging a bit- but that was not the problem. Anybody else had this problem??

 

Looks like your driveshafts or boots do not fit your car. I would replace asap.