Did you ever end up getting a resolution on this? My best take on this is that it has to do with the version of SQLyog that you’re running. Seems to work without the bugs on the v12, v13 has this issue I believe.
I am running SQLyog Enterprise v13.1.0 64bit and it has this problem. It’s frustrating to have to go back and fix every function call in a query.
I’d also like some more control over the formatting engine to tune it to my style. For example; detect the AND following a BETWEEN and keep it on the same line. Just being picky there.