So now I can get unique files, hurrah! but it seems the second file is plotting both the first and the second plot, the third is plotting all three, fourth is plotting all four, etc. here is the new code:
for j in range(2):
dhulist=pyfits.open('test.fits')
row=5
colum=j
ax=[]
val=[]
for i in range(1600,3040):
val.append((dhulist[0].data[i,row,colum]))
ax.append(((((dhulist[0].header['CRPIX3'] -i)*(dhulist[0].header['CDELT3']))+5000)/1000))
plt.plot(ax,val)
#plt.show()
plt.savefig("5_{0}.png".format(j))