OpenGL timer query problem

opengl-timer-problem.c

glBeginQuery(GL_TIME_ELAPSED, gQueries[gQueryBackBuffer][TIMER_RENDER]);
GL_ERROR("begin RENDER timer");

{
    world.timer = ms;
    nocull.timer = ms;

    /* start a batch and render */
    gfxBatch(&world);
    gfxRender(&sheet, &nocull, &waveShader);
    gfxRender(&axis, &world, &colorShader);
    gfxRender(&crystal, &world, &shader);
    gfxRender(&cube, &world, &colorShader);
}

{
    gui.timer = ms;

    gfxBatch(&gui);
    gfxRender(&quad, &gui, &guiShader);
}

glEndQuery(GL_TIME_ELAPSED);
GL_ERROR("end RENDER timer");

glQueryCounter(gSwapQuery, GL_TIMESTAMP);
GL_ERROR("set timer");
GLint64 timer1 = 5;
glGetInteger64v(GL_TIMESTAMP, &timer1);

uint32_t beforeSwap = SDL_GetTicks();
SDL_GL_SwapWindow(window);
uint32_t elapsedSwap = SDL_GetTicks() - beforeSwap;

GLuint done;
glGetQueryObjectiv(gQueries[gQueryFrontBuffer][TIMER_RENDER], GL_QUERY_RESULT_AVAILABLE, &done);
if (!done) trace("render timer not done\n");

done = false;
while (!done) {
    glGetQueryObjectiv(gSwapQuery, GL_QUERY_RESULT_AVAILABLE, &done);
    GL_ERROR("check");
}

GLuint64 timer2;
glGetQueryObjectui64v(gSwapQuery, GL_QUERY_RESULT, &timer2);
GL_ERROR("fetch result");

/* collect the timers of the frontbuffer before swapping the query set */
GLuint64 timerRend, timerSwap;
glGetQueryObjectui64v(gQueries[gQueryFrontBuffer][TIMER_RENDER], GL_QUERY_RESULT, &timerRend);
// glGetQueryObjectui64v(gQueries[gQueryFrontBuffer][TIMER_SWAP], GL_QUERY_RESULT, &timerSwap);

printf("render objects: %f ms, CPU stall: %f (%u) (%"PRIu64" - %"PRId64" = %f)\n", timerRend / 1000000.0, timerSwap / 1000000.0, elapsedSwap, timer2, timer1, (timer2 - timer1) / 1000000.0);

/* swap the query set */
swapQueryBuffers();