Good to know I wasn't totally wrong. I didn't think it was a deal breaker, and I knew they'd obfuscate the the Skeksis origin, but it didn't seem quite right.I watched the entire series over the course of the long weekend, and I really liked it. This is after watching the movie last week in preparation.
I too thought that some of what they did in the first few episodes was contradictory to what happens in the movie, but later in the series, things start lining up a bit more. My only (minor) complaint is the extra emphasis on Augrha and the fact that she's this uber-character similar to Elminster or Gandalf. Again, though, it's only a minor quibble.
I really liked the fact that at one point in the series, you can actually see the D&D party being formed. You can look at it and say, "There's the fighter, there's the barbarian, the podling is the paladin...that guy right there is definitely the bard...oh, and she's the druid."