This is a very interesting question. I just spent an hour researching it on the Internet as best I could.

Unfortunately the official ISU Grand Prix Announcement for that year (2207-08) is missing from the archives on the ISU website. However, the official rules for each event separately are still there. Here is Skate America, for instance.
http://www.usfsa.org/content/events/...ent%202007.pdf
If you scroll down to the last paragraph on page 7 you will see the rule that says, if a team is skating in their non-scoring event and finishes higher than someone else, the lower-finishing skater (like Vise and Trent) does
not move up and get the points for the higher finish. So this was an actual rule for 2007-08 (and also for 2006-07).
This article from the Golden Skate archives mentions that
http://www.goldenskate.com/articles/2007/sa_1.shtml
From what I have uncovered, I think the rules were gradually changed over a three or four year period to give the ISU greater and greater control over the Grand Prix series, vis-a-vis the organizers of the individual events. In 2006-07, for instance, the rules permitted
any skater to skate in a third, non-scoring, event, if he/she was invited. (Sasha Cohen did so, for instance.) The reason for this is that the individual event organizers wanted to make money from television and the live gate, so they wanted to be able to invite the top draws in all disciplines.
By the 2007-08 season, the ISU was tightening its control and they changed the rules to prohibit singles skaters and ice dancers from doing more than two events. Pairs were allowed an exemption to the new rule because there were not enough top-flight pairs teams to go around. This loop-hole for pairs was closed by a rule change the following year (2008-09).
There were a bunch of other rules changes during those years, all designed to require skaters to toe the line laid down by the ISU and correspondingly restricting the rights of the event organizers to do whatever they wanted to, as had been more-or-less the practice in the past. Some of the individual events pre-dated the Grand Prix series, and the organizers of Skate America and Skate Canada, at least, dragged their heels as much as possible in complying with the new rules.
Some of these new rules were that skaters could not skip Grand Prix events and appear in shows and cheesefests instead, that skaters could not appear in the exhibition if they didn't skate in the competition, that skaters who performed in the gala must do a real exhibition program, not just repeat their short program, etc.
So if you ask
why the rules were changed several times. I think the answer is only partly to make the competitions more fair. It was also part of the ISU consolidating control.
The issue that Tony Wheeler, Watchvancouver, Gsrossano, Nylynn, etc., are raising on this thread is quite a bit different from the question of why the ISU changed the Grand Prix rules in 2006 and and again in 2007 and again in 2008. In the case of the 2010 Junior Worlds, the rule is clear and as far as anyone can tell the ISU violated its own rule.
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