By the way, I found the solution.
If anybody is interested, you should catch the exception happening in glGetError(), it's because LWJGL makes GL calls before the context is current and GLIntercept doesn't really like it (it's a known issue). Other than that it seems to work fine.
I would strongly suggest to use
GLSL Devil instead though, it's much better, has GUI, and doesn't have the aforementioned error.