Sounds like what I experience with a few games, like Xexex, until I turn frame_delay on the game runs like about 200% indeed.
Dunno if related but it could maybe: after you've just set vsync_offset for a game, then go back to the menu and select a different game; the previously set offset value is carried over, like it stuck to the slider and remains until you reset it or set a new value.
Specific ini files experienced a similar issue until 203 where it wasz fixed after I reported it.
These are problems I've mentioned not long ago, and BTW I also experience random crashes on games launch from time to time, maybe it is related.
PS: if you always use command line instead of the UI it is possible you don't experience such issues.