What could be causing my three way switch to malfunction?
You have a simple mis-wire somewhere. As previously stated, you need to open both switches and see how everything is wired. Get a few good diagrams of common 3-way wiring patterns and see if one is like the way yours are wired. A Google search will bring up many.
The position of the switches does NOT matter at all. What matters is identifying the feed wire, the load wire and the travelers. In many cases even colors don't matter (or at least are not consistent).