This is related to the post here:

https://www.klayout.de/forum/discussion/1539/cif-visualisation-glitch-and-writing-bug-with-a-cell-rotated-by-5-degrees#latest

The reader bug consists of creating a box with coordinates 0,0..0.999,0.999 instead of 0,0..1,1. It is reproducible on Windows 10, 64bit.

Writer bug: Saving the file will render an invalid transformation. For example here:

C2 R9.00719925474e+15,9.0370723779e+14 T0,0;