I've used Valve Hammer Editor v 3.4 for a few years now and I've never encountred this problem before. I open a particular file, and a great number of vertices are slightly misplaced, most no longer snapped to grid. Of less concern, but greatly suspicious, all objects that were grouped are now ungrouped.
It may be coincidence, but I've also noticed that the only polygons with misplaced vertices are those that were created a while ago, whereas the newly created objects are fine.
The are a great number of vertices on this particular model, however I haven't tried to do anything crazy to the thing, like rotation or translation of the entire collection of objects. Like I said, I've used the program a fair amount and this is unprecedented. Any ideas on what is going on?