I load .40 S&W (along with .45 ACP, .45 Colt. .38 Special and .357 Magnum) on the SDB.
The SDB does not re-size the bottom 1/8" or so of the case, but if the sizing is not screwed all the way into the plate it may not be doing all it can - so check that first.
Did the guy's brass start out as new - or used brass? Has it been fired in any other gun?
Even though you say its not "glocked" brass if it was fired in a larger chamber you may still need to get the brass fully sized the first time (I use the Redding GRX) so you can run it trough the SDB and have it properly chamber in other chambers.