Periodic thread fails real-time in Xenomai

I'm creating a periodic thread which outputs a square signal on an analogic output. I'm using Posix Skin and Analogy from the Xenomai API.

I tested the real-time performance of my code using an oscilloscope and looking at the latency on the square signal (whose frequency is 1kHz). I am supposed to achieve <100us latency. However, the signal is strongly (>250us latency) perturbated by common interruption signals, like moving the mouse, starting a new program, etc.

The flags in my makefile are set up as such:

gcc  -I/usr/xenomai/include -D_GNU_SOURCE -D_REENTRANT -D__XENO__ -I/usr/xenomai/include/posix    
main_posix.c -Xlinker -rpath -Xlinker /usr/xenomai/lib -Wl,@/usr/xenomai/lib/posix.wrappers 
-L/usr/xenomai/lib -lpthread_rt -lxenomai -lpthread -lrt  -lanalogy -lrtdm -o main_posix

and this is the code:

#define PERIOD 1e6 
#define FILENAME "analogy0"
#define ANALOG_SUBD 1
#define CHANNEL 0
#define SCAN_SIZE 2
#define DELAI 5

static char *filename = FILENAME;
static int idx_subd = ANALOG_SUBD;
static int idx_chan = CHANNEL;
static int valueUp = 450000;
static int valueDown = 98500;

void *TaskCode(void *arg)
{
   unsigned char sgnl = 0;
   unsigned long overruns_r = 0;

   a4l_desc_t dsc = { .sbdata = NULL };
   a4l_chinfo_t *chinfo;
   int err = 0;
   unsigned int scan_size = SCAN_SIZE;

   err = a4l_open(&dsc, filename);
   if (err < 0) {
        fprintf(stderr,
            "insn_write: a4l_open %s failed (err=%d)\n",
            filename, err);
        return NULL;
   }    

   while(1) {
        pthread_wait_np( &overruns_r );
    if(sgnl)
        err = a4l_sync_write(&dsc,
                 idx_subd, CHAN(idx_chan), 0, &valueUp, scan_size);
    else
        err = a4l_sync_write(&dsc,
                 idx_subd, CHAN(idx_chan), 0, &valueDown, scan_size);
    if (err < 0) {
        fprintf(stderr,
            "insn_write: a4l_sync_write failed (err=%d)\n", err);
        goto out_insn_write;
    }

    sgnl = (sgnl + 1) % 2;
   }

   out_insn_write:

    if (dsc.sbdata != NULL)
        free(dsc.sbdata);

    a4l_close(&dsc);

    return NULL;

}

int main(void)
{
   mlockall( MCL_CURRENT | MCL_FUTURE );

   pthread_t thread;
   int rc, i;
   int prio = 99;
   struct timespec rqtp, rmtp;
   rqtp.tv_sec = 0;
   rqtp.tv_nsec = PERIOD;

   struct sched_param sparam;
   sparam.sched_priority = 99;

   rc = pthread_create(&thread, NULL, TaskCode, NULL);
   assert(0 == rc);

   rc = pthread_setschedparam(&thread, SCHED_FIFO, &sparam);
   assert(0 == rc);

   rc = clock_gettime( CLOCK_REALTIME, &rmtp );
   assert(0 == rc);
   rmtp.tv_sec = rmtp.tv_sec + DELAI;   

   rc = pthread_make_periodic_np(thread, &rmtp, &rqtp);
   if(rc == ETIMEDOUT) printf("Début dépassé \n");
   else if(rc == ESRCH) printf("Thread invalide \n");
   assert(0 == rc);

   rc = pthread_join(thread, NULL);

   exit(EXIT_SUCCESS);
}

I am strongly suspecting (by looking at the Xenomai scheduler) that my program somehow enters secondary mode. I tried to remove the "assert" statements as well as the relevant printf's, but this was not successful. Any idea how to fix it?

As always, the devil is in the details.

I enabled the -Wall option in gcc, which shows all the warnings. It turned out the headers for pthread_* were not properly loaded, which prevented me from seeing that the first argument of pthread_setschedparam was wrong, and was supposed to be thread and not &thread.