Missing filament in infill

Sorry for the question, it is probably something very simple but I got a Prusa Mendel 2 i built couple months ago. I keep having issues with the infill of the test cube. I followed the wiki to calibrate the printer and I believe I did the best i can with it lol. Could anyone help me figure out what exactly is wrong? I don't fully understand slic3r settings yet so maybe it has to do with some configurations there?

Thanks

That doesn't look like an infill problem, it looks like your first layer isn't being laid down correctly. When your Z-Axis is at its lowest point, you should just barely be able to get a sheet of paper under the nozzle. Have you calibrated your Z-Axis height? If it's even a little too high, the plastic will cool too soon, and your layers won't get laid down correctly.

I did the calibration again and the outer layers seem to print better. But the inside layers actually got worse.

So seems my print bed us not actually flat. On the corners the nozzle is calibrated but once it moves to the center the nozzle touches the glass. Would this be the glass not being flat, or the wooden bed I made that holds the heatbed?

Thanks