What GMT version is this? (gmt --version). There are two gmt project calls in your script, do they both give you that warning about latitude-formatting?
Also, I am not sure I understand what you want. You say you have Cartesian coordinates and you want to run project, but then the output from project (cross.dat) is being plotted with what looks like a geographic region (-R-180/179/-86/89) and a Cartesian scaling. If x and y are actually longitude and latitude, what is up with the Cartesian treatment? And if they are not, is it just coincidental that you are using a -R that looks like it is geographic degrees?