WORKAROUND THAT WORKS:  for dual return files (self/spouse):

For all T3s: enter 100% ownership at top and then half of all values into boxes.  (I also only entered capital gains in box 53, using the same value as line 21, half the total, instead of dividing the time periods).

Then values for line 68140 on T936 were correct and agreed with Schedule 3 line 17600, and I could NETFILE both returns. 

@Genie45 For the error on the T3 slip not balancing box 52+53 to equal box 21A, trying to enter the sum of 52+53 into box 53 (deleting 52) should fix the problem.