I'm assuming that you're using the same BB bastard BBs through your rifle and other guns?
The sensors of a chrony work on detecting a drop in light (photon mumbo jumbo) hitting the receptor (i.e. the shadow of the bullet/bb)...so the following can affect it:
1. Dust in the air
2. Incidental shadows (i.e. the light from the stairway was giving me screwy readings once)
3. Intensity of the light (i.e. my old red shooting chrony doesn't have any smarts and I'll get different readings if there's just barely enough light to get a reading vs. a good strong source of light)
4. Dust in the sensors
5. "Shadow casting" nature of the projectile
2/3/4/5 would be consistent during a given shooting session...1 could vary depending on whatever is going on at the time (I do woodworking as well and it plays havoc with electronics).
Ideally you would have a light positioned directly (and diffused) over each sensor and high enough so that the light from one bulb wouldn't be able to hit the other sensor directly (this happens to mine if the bulb is over the rear diffuser...it kind of shines un-diffused? onto the front sensor).
I've set my chrony up in an old tool box with a backstop box inside. It tends to help with the consistency of chrony-ing in my basement. The light is positioned more towards the front sensor so that the rear screen "screens" the rear sensor.
But I think I'm going to throw in the towel...and get one of the madbull chrony's from Jugglez. I'm getting tired of setting it up and just want to stick the muzzle a set distance away from the front sensor and pull the trigger. (Plus...I want to see what the ROF of my CQB rifle is...
All of the above probably doesn't help...but I hope it does.