Wanted to say this method also worked for me. I had originally used the 50/50 split for our joint (me/wife) T3's and the CRA rejected my submission with the code 95365
On inspection I saw that T936 Chart A line 68140 reflected the correct 50% split of all Box 21 Capital Gains.
But on schedule 3 lines 17599 and 17600 (which reflect the Capitol Gain period totals for boxes 52 and 53 respectively) it used the full unsplit amount. Hence the reconciliation error.
So, I went back to the T3 slip entry's and created the split (50/50) manually for each of us making sure the allocation for each entry was 100% (that's the default). I verified the form numbers T936 and Schedule 3 for both my wife and I and before submitting went through all the "Easy Steps" to make sure the software could do whatever updates it needed to. NETFILE was successful.
