First of all let me start by saying I am not a rates expert.
Here is my attempt to explain what I see from the details you have provided.
3. 9 - 20 Feb 2009 (Tix issued on Nov 24, 2008)
YYZ --> YVR --> NRT --> SIN --> NRT --> YVR --> YYZ
Fare (incl. Navcan/Surcharges): $1359.00Taxes & Fees: 6.55 (CA) + 43.18 (XG) + 51.59 (XT)
Total Fare: $958.32 + Change Fee/GST: $52.50
Fare Calculation: 03OCT08YYJ AC X/YVR AC YTO Q23.00R231.00AC WAS Q7.50R545.00AC YTO Q7.50R545.00CAD1359.00 END ROE1.00 XT31.88US5.17XA7.24XY2.59AY PD9.34CA32.48XG30.00SQ XF4.71IAD4.50
4. 9 - 20 Feb 2009 (Tix issued on Dec 10, 2008)
YYZ --> YVR --> NRT --> SIN --> HKG --> YYZ
Advised by staff that I can route to HK for the same fare / do stopover for $52.50
Fare (incl. Navcan/Surcharges): $1674.00Taxes & Fees: 1.11 (CA) + 443.51 (XT)
Total Fare: $759.62 + Change Fee/GST: $105.00
PRF125.75CAD/RCN 15475653
Fare Calculation: 09FEB09YYJ AC X/YVR AC YTO Q21.61R217.04AC YVR Q21.60R172.87AC X/YTO AC SIN R323.20AC X/HKG AC YTO Q4.22R811.77NUC1572.31 END ROE1.064330 XT420.00YQ23.51SGPD15.89CA1.50XG30.00SQ
Looking at the above details only...I can see that the $759.62 is reached by taking your base fare in item 4.9 minus your base fare in item 3.9 then adding the additional ca tax $1.11 and adding the taxes/surcharges for the international ticket. So the long calc would be
$1674.00- $1359 = $ 359.00 additional base
add dif in ca tax $1.11
add int'l surcharges $443.51
total adcol $759.62$ plus change fee
also appears that you got a part refund of 125.75 which would be for your unused taxes/airport fees.
Pls note, I do not consider myself a fares expert...this is just what I can see from the calculations that you provided.
I must say that the reason you were told you are not allowed any changes is most likely to do with the fact that somehow someone allowed you to use an expired ticket beyond the ticket extension validity allowances.
I am however confused by the amounts you mention for change fees on each item. Have you made a change to your original trip before cancelling the ticket? I am not sure why you show a change fee there.
Also looks like the next changes you made you were charge only 1 change fee each time instead of 50.00 cad pls tax per direction. Just an observation.
Hope the above makes a bit of sense to you. Not actually seeing the file and not being part of the conversations, I cannot give you more than that.