There are only a few things I could think of.
- As 99warriornj posted, they have to be installed with the reinforced ridge towards the top, that thicker rubber is there to support the weight of the carb hanging on it.
- Being too rough installing it and working on the carb. They're fragile and if you have to force it, bend it, etc. that can crack it.
- Broken upper motor mounts causing excessive movement and vibration.
- Incorrect alignment of boot between airbox and carb causing continual stress on manifold
- Air filter mounted directly on carb without airbox, continual stress on manifold
Are you getting factory yamaha manifolds or cheaper aftermarket ones? My local shop started stocking an off-brand manifold a few years back because they were a few bucks cheaper than the Yamaha parts and looked the same, but everybody that was buying them was bringing them back a month later so they went back to genuine Yamaha ones.