Tax Installments arent deducted from tax payable

I am a non-resident who has been paying tax installments against rental income.  When looking at the PDF copy of my return I see that my tax installments dont appear to be deducted from my Total Payable, and my Balance owing equals to Total Payable. When i look at the line item for Total non-resident tax witheld, it shows a blank value. I indeed entered values for the tax installments, and i can clearly see them on the input page, they are just not applying in corresponding field in PDF, resulting in a wrong Balance Owing (when infact it should be a Refund). I can see correct values though, in the top left corner of the screen with the Refund Preview. im not comfortable to submit the netfile, thinking that perhaps the wrong values will be submitted to CRA. What could be the issue?