To measure focal plane shutters, ideally two sensors are required, to measure both curtains. It is possible to use a single sensor & move it from right to left, or top to bottom, but that is a bit of a faff.
The OP has not described their shutter tester or provided any photos, so it could be sometimes he is measuring first curtain and other times second curtain? Just a thought.
There are many homebrew shutter testers out there, I'm not going to get into the debate of which is best or pass comment on any of them.
Will say that my own tester, look for the 'build a cheap shutter tester that works' in this section works perfectly with 35mm focal plane shutters. I started the post to help people build a cheap tester (that works).