I have never had that problem. I have used hundreds of Jantz's Corby bolts.
Try this:
Check the depth of the female shaft hole against the male threaded part ( use a toothpick) - Is the hole deep enough?
If the hole is deep enough, take two screwdrivers and try to seat the two halves together. There may be a slight bind stopping the fit. Make sure you aren't cross threading them.
If the hole isn't deep enough, or the two parts can't be screwed together, call Jantz.
It is OK to shorten the bolts, but unless there is a special situation, you should remove equal length from both halves.
When a Corby is a proper fit, the female part will go through the scale and tang, and stick out about 1/32-1/16" on the other side of the tang. The shoulders of the bolt holes should be 1/8" above the tang. This allows the bolt to tighten the scales to the tang with just the right amount of clamping pressure. Only tighten the bolts enough to be snug, over-tightening can tear or split the wood.
Final tip :
DRY FIT everything before applying any epoxy. All should be snug and show no gaps. If it needs fixing or adjusting, do it now.