Clive, you're experiencing a classic frustration with Animator--namely, that prescribed motion won't behave as it ought with Animator. Which version are you using?
Here's how to solve the problem (maybe). The only possible fix for things like this is to confine all possible directions of motion except one. So to rotate something, it must not be able to move in any other possible direction. If you need that part to then move in another direction/axis, you must use a different part--or your motion will randomly flip in the way you're currently seeing.
When I do this, I actually add other parts to the assembly with their extremely limited motion directions. So let's say I need to animate a tail gate (such as we see at Tommygate.com--those were done in Animator). I have rotational motion to open the gate, but then the gate unfolds and then drops to the ground. This takes many, many parts in the assembly, which are all carefully limited in their particular motion. I start with the rotating open tailgate, which can move only 90°. It makes its rotation, I show the next tailgate waiting in place for the next motion type (unfolding) and quickly hide the "old" rotating tailgate (I use increments of 0.1 seconds for hide/show items, so they're not visible in the animation). I then unfold the tailgate through its 180° unfolding, quickly show the next tailgate, quickly hide the "old" unfolding tailgate. I then lower the newly-shown tailgate.
Note that each of the repeating elements above can move in only one way at a time, and is otherwise constrained by mates. Angle and limit mates constrain the degree of motion given in the motions allowed.
This method gets very confusing, and has its own problems with other Animator bugs, but after you've carefully crafted a script to follow to avoid your own confusion while building the animation (you cannot edit such an animation, or the whole thing will fail--it must be done right the first time), this sort of thing is possible. The animations I did at Tommygate.com are proof.
Good luck.
Jeff Mowry
A people who value security over freedom will soon find they have neither.
