Here is the confusing part:
I was travelling with my
family from BOS to SEA on July 20, 2008. The record locator for these
trips are
****** 2 pax
****** 1 pax (myself)
I had requested upgrade
for IAD-SEA leg only for all 3 pax and had requested to use my 500-mile
upgrade. I have 16 certs in my account. The distance with IAD and SEA is
2306 miles and should be covered by a total of 15 certs.
Nonetheless,
while checking in at BOS airport I was told I was upgraded (******)
using 5 certs. But for my family the agent incorrectly requested 6 certs
each. This made my account short by 1 cert. Instead of listening to my
argument that the IAD-SEA leg which is 2306 miles requires only 5 certs,
the agent wanted to sell me 4 certs for $200. It was like a used car
salesman
s opening salvo.
I believe BOS-IAD-SEA upgrade WOULD require 6 500's (1 for the BOS-IAD seg, and 5 for the IAD-SEA seg).

But you say you were ONLY upgrading IAD-SEA, and that you were told while checking in at BOS, that you needed 6 certs. The agent must have been thinking BOS-IAD-SEA rather than just IAD-SEA for the upgrade? Somewhat understandable mistake, but the agent should have listened to you when you tried to correct the error, certainly. @:-)
As for the other problem, the early boarding of someone who you believe was not "entitled," well, I would just let that one go -- even if you had NOT been compensated as you were!