My chronograph is a Shooting Chrony that is many years old. It was purchased about 20 year ago or thereabouts.
My first outing with a muzzle loader gave me quite a shock. The chrony was reading bullet speeds of around 300 fps. Then it dawned on me that the chrony was reading the last object through. I had placed the chrony quite close, because like you i wished to know the 'muzzle velocity'. The sabot separated from the bullet right away after they left the muzzle, and the chrony was displaying the speed of the sabot, not the speed of the bullet.
This forced me to place the chrony about 20 yard away, because by then the sabot is nearly on the ground, and then the bullet was the only object passing over the 'eyes'. Knowing the bullet speed at 20 yard allowed me to find the muzzle veloctity by using a ballistic program.
Here is one of the ballistic calculations:
How this particular program is used, is one inserts the muzzle velocity to find the ballistics. In my case i didn't know the muzzle velocity; i knew the velocity at 20 yards was 1899fps, so what i did was guess at the muzzle velocity a few times until the program calculated the correct velocity at 20 yard. Now i 'know' the muzzle velocity even though i was unable to measure it because the sabot separated from the bullet right away.
Some here say their chronograph measures the first object through. If that is the case with yours you could place your chronograph very close if it has a protective shield.