If the chronograph is not wrong... you little scale must be doing the job.
That said, if it's an electronic scale I'd probably want to "check and balance" it with a beam scale... if it's a cheap Lee beam scale, they actually work, and can be depended on... you didn't say what kind of scale it was.
As to the identical numbers...
I have seen this, especially with my .308 win loads when I get to a good powder level.
I have an F1 Chrony, so that might be part of the reason for identical numbers... I was shooting some .308 loads, 168 grain SMK's with 43.6 grains of IMR 4895 across my F1 and I got three 2599's in a row, then a 2601... and another 2599...
This said, the chronograph cannot and should not be depended on for load proofing. I know that many people do, but the target must always be the final arbiter.
For those who don't have good access to long range shooting areas, a chronograph is the only way to hazard a guess as to what your vertical will be at say, 800 yards. But again, actually shooting paper at the longest range you plan to use the rifle is the only sure way to know what it's going to do in the field.