We are having very similar problems with 10.5.1 + and what appears to be inconsistency and instability with the pyramids tool. Sometimes they are successful and other times not. Successful meaning the tool reports they are built only to get prompted the pyramids do not exist or simply not seeing anything at smaller scales. Other times we are presented with this warning and have never run into this before? "C2018_MOSAIC_BLOCK1: The display area covers too many pixels at the current display resolution. Please zoom in or build pyramids." This is coming up with clicking on the raster layer and clicking "zoom to layer".
Older software releases prior to 10.3 did not appear to have this problem with our past collections in File or SDE GDB.
I am curious what settings are you using for pyramids? Applying any compression on them?