Well, it's completely normal that your emulation speed is not 100% for many games, as we can't tweak the AVGA3000 video modes under Windows. If we want smooth scrolling, everything must be forced to run at 60 Hz, because that's the refresh that most AVGA3000 modes are defined. This will cause acceleration or slowdown depending on the original game's speed.
The triplebuffering in GroovyMAME just ignores the video card refresh and just relies on CPU clock, that's why it runs at perfect 100%, but scrolling is ruined.
As an alternate solution you can try the GroovyArcade Linux live-CD, this one can reprogram ArcadeVGA3000's modes so the result is perfect.