Two threads ping-ponging work between them causing CPU frequency to drop since none of them are 100% busy

Question

The background for my question is that I have a game engine whose main rendering loop involves two threads: In short, one thread generating OpenGL commands and another thread that takes the generated OpenGL commands and dispatches them to the driver. This allows them a certain degree of overlap of the work, but they still have to wait for each other at certain points. This is of course a fairly specialized situation local to me, but I also can't imagine the situation of having two threads ping-ponging work between them with a limited degree of parallelism is a particularly uncommon scenario.

Now, my problem is that, since none of the two threads are 100% busy, but rather spends some time sleeping waiting for the other thread to catch up, my OS scheduler apparently thinks that I'm not using the CPU enough to clock it up to maximum frequency. In marginal situations, this causes me to drop FPS significantly. This is on Linux with the default powersave cpufreq governor. Setting it to performance makes the problem go away entirely, but that's obviously not the default, and not what other people will be using. I don't have any Windows systems readily available to test on, so I don't know if Windows' scheduler has a similar behavior. My program is written in Java, but I can't imagine that to have any significant bearing on the problem.

Again though, I'm sure I'm not the only one with a program that behaves in this manner. Has someone else had this problem? Is there a good way to "solve" it? It seems a bit unnecessary to be dropping performance significantly just because the operating system doesn't really understand that the CPU is in fact being used to 100%.