The simplest thing to try – and thus the first thing to try – is rearranging the order you load the plugins. It sounds silly, but sometimes it helps.
However, I only give that a fairly small chance. After that, it's time to figure out what is going wrong. If both plugins truly conflict in the sense that they are writing over each others' variables, you have a problem.
I never encountered this before, but my first idea would be trying to trap each plugin in a closure. That way, whatever (formerly) global objects they shared (that caused the interference) are now within a plugin-specific closure. You'd have to think about how you can make the plugin available from outside that closure then, though.