How about a Timer library that works properly?
DueTimer does not get the requested interval correct,
giving 49000 us when asked for 50000 (off by 1 ms).
How about submiting an issue on the GitHub so that I can know about it, and try to fix it?
Remember that micros() has an very weird reading too... and it doesn't works properly. The correct way (maybe the one you used), is to use an osciloscope...
Also, make shure to notice that DueTimer tries to find the Best clock for the desired frequency. However, it might not be EXACLY to what you want...
If you can, try to set the timer to 51ms, instead of 49, and see if it works. If yes, than we have a bug...
But make shure to submit it on the issue page, please! https://github.com/ivanseidel/DueTimer/issues?state=open
Have just tested it with micros, and it's showing up exacly 50000uS.
Can you send me your code?