I have two questions:
1- Are you making box joints or finger joints? To me, for joining box corners, you want to make "Box Joints". Box joints have square ended pins and are used for making box corners.. Finger joints have tapered pins and are used for joining boards end to end to make the resulting board longer.
2- What kind of plywood do you have?
You will need "void free" plywood for making boxes and cabinets using "Box Joints". Baltic Birch and Marine quality plywood has no internal voids so they do well for making boxes and cabinets. Construction plywood has internal voids and does not make good joints with the Incra I-Box jig.
I use my Unisaw with My I-Box jig because I've found that I can get cleaner cuts using my saw and the SBOX8 blade than I was able to get easily using the jig on my router table. This is because the saw blade cuts in only one direction as it passes through the work. A sacrificial piece in the I-Box jig becomes a zero clearance insert, keeping the blade from breaking the edges of the cut on the back side. When cutting with a router bit, the rotation of the bit cuts in both directions as it passes through the work. To get chip free edges on both sides of the cut, a second sacrificial piece must be added to the back side of the work as well, so both sides are protected as the cuts are made.It can be done, but I find that it's easier, faster, and produces better results if I use my I-Box jig on my table saw.
Earlier this year I made about 20 boxes from Baltic Birch plywood, joining all of the corners using my I-Box jig on my Unisaw. I had perfect results. Plywood can be used to make boxes and cabinets, if the plywood is void free and you use sacrificial pieces to prevent tear-out. If your plywood isn't this good you should find another way to join the pieces. Solid wood corners with plywood panels between is one way.