When installing hinges on small boxes, I utilize the flip stick that you describe in your books and in a Fine Woodworking article. This procedure hasn't failed me as long as I cut the stick accurately. Where I have problems is in trying to center the pilot hole when using very small hinges that utilize no. 2 brass screws or smaller. This seems to be especially difficult in woods with prominent grain - no matter how precise I try to be, it seems that the awl never finds the exact center and I'm sure you know how a small error here can mess up your hinge alignment even with accurate mortises. The I have to sand the sides and/or top to align with one another, With larger hinges, I use Vix-type bits to center the pilot hole but haven't been able to find one that small.I wish they made a vix bit in the right size. The interesting thing about butt hinges when they are enclosed in a mortise on three sides is that the mortise will hold them in position even if the screws are slightly misaligned except when the screw is slightly misaligned toward the outside of the box in which case the screws pull the hinge away from its proper position. My answer, is to make sure that the screw hole is either dead on or slightly offset away from the back side of the box so that it pulls the hinge into position rather than away. When using an awl, make sure the hole is exactly where you want it before you drill, and this may take close observation and a bit of prying, particularly when the wood is heavily grained.
You you have any suggestions that would facilitate properly aligning the pilot holes?
There is another problem with butt hinges that may be causing part of your problem. Sometimes on less expensive hinges the leaves may not be in exact alignment on the back side. So you need to check them carefully, and file them even on the back I show this in an earlier post "Hard to see but explains a few things."