Linear pattern for extrude cut faces goes bananas

Hi guys!

So I'm working on this part and at the end I used linear pattern to copy the extruded holes.

At first it looks ok, but if i save the file - exit solid - enter and load the files again it looks like in the attached pic (all messed up).

I'm not really interested in creating every hole (over 100) manually

Any ideas ?

See file attached as well (solidworks 2012)

Thanks!