Hi, professional physicist de-lurking here. There's something I don't understand, and pardon me if this has already come up. Newton's Laws inherently include energy conservation. Every force (mechanical, chemical, electromagnetic ...) can be calculated as F = -dE/dx: the force in any direction is equal to the rate of change of stored potential energy with respect to displacements in that direction. If you have a system with a lever sticking out of it, and the system's energy goes up by 50 joules when you displace the lever through 2 meters, then the lever will resist that displacement with a force of 25 N. If there isn't a conserved energy which changes, there won't be a force. For example, the gravitational force F = -mg can be derived from the gravitational potential energy, E = mgz +C (where z is the height, g is the acceleration due to gravity (taken to be positive)), so Fz = -dE/dz = -mg.
Ditto for kinetic energy: if you exert a net force on an object, and maintain that force F while the object changes position by dx, you change the object's kinetic energy by dE = F dx. Notice that, to actually apply that force, you had to decrease the potential energy in some other system---and that the KE increase exactly equals the PE decrease. If there wasn't a change in PE, then there wasn't a force. If there wasn't a force, then there wasn't an increase in KE.
This is true even for frictional forces: the force exerted by a brake pad is equal to the increase in thermal energy of the pad and rotor. The only difference is the irreversibility; you can increase thermal energy as much as you like, but you can't freely turn it back into kinetic or potential energy.
So, AgingYoung, you've got a simulation package with Newton's Laws built in, laws which do nothing but conserve energy, since they never exert any forces at all unless they have a potential energy store to sap. If you think that some aspect of your simulated system is picking up energy---well, I presume you must think that there's a subsystem, linkage, or doohickey for which F is not equal to -dE/dx.
Is this true? If so, what makes you think F=-dE/dx would break down in your system? What makes you think Working Model includes this breakdown in their underlying physics code, rather than actually calculating the conserved potential energy for each of your components, and calculating energy-conserving forces from there, thereby guaranteeing that the full system will conserve energy?
It seems to me that your task---twisting a Newton's Law simulation and hoping a non-Newton's Law result pops out---is rather like playing with a calculator and trying to find two odd numbers whose product is even. Sure, you may find some round-off error or approximation that gives the appearance of success, but why bother?