I also use a couple Better Beamers without any problems. I use them on Canon 550EX and 580EX II flashes.
Perhaps you aren't using a long enough telephoto lens? Needs to be minimum of 300mm on full frame or 200mm on APS-C crop sensor, or 150mm on m4/3 sensor. That's the bare minimum, though. Longer is better. Mostly I use with 300mm and up to 500mm on crop sensor (equiv. to about 500mm to 800mm full frame). Also sometimes with 2X teleconverter on 300mm and 1.4X teleconverter 500mm (equiv. to about 840mm to 1120mm on full frame).
I usually put the flash on a flash bracket when using the Beamer. I have a couple Wimberley brackets made just for this sort of thing... attach Arca-Swiss plate on the tripod foot of the lens. These brackets can be seen on their website:
www.tripodhead.com. They're modular and can be configured several different ways, but do a good job positioning the the flash very precisely.
A couple other things that may or may not help...
I usually use fill flash... not full flash. It's also usually with High Speed Sync, which further reduces flash power.
This is an example using the Beamer on one of my flashes (with a little "ghosting", using APS-C camera with 500mm + 1.4X... 1120mm full frame equiv.):
Here's another where I used some gentle fill flash with a Beamer (APS-C with 500mm... 800mm full frame equiv.):
For the image below I ended up using a 200mm lens (on film... so full frame), and used flash without the Better Beamer:
Here's another where I used fill flash without the Better Beamer (300mm lens with 1.5X teleconverter on full frame/film):
Also, I've made a couple extra panels out of poster board, attached some Velcro and use those to fully enclose the Better Beamer, rather than leave it open top and bottom.
Finally, I agree that it may help to set the flash to 50mm (i.e., don't let a dedicated flash change it's focal length setting on you... override itt). But to be totally honest about it, I often forget and it hasn't caused any problems for me.