LAUNCHXL-F28P55X: CLB ClearFIFO doesn't clear the FIFO

Tool/software:

I'm using HLC to push data to the FIFO of CLB1

I can properly read the data using 
CLB_readFIFOs(CLB1_BASE, g_fifoBuff);
for(i=0;i<CLB_FIFO_SIZE;i++) {g_fifoBuff[i] = 0};
CLB_clearFIFOs(CLB1_BASE);

when CLB_readFIFOs is called it will return the memory content that was in ther last time.

however it seems to have the effect that any new data will be placed in g_fifoBuff[0], higher indexes only used when events occur faster than I'm polling