I find that Garuda and a few other big airlines are fumbling trying to catch up with LC Carrier such as Air Asia in the IT or online services. I often get frustrated trying to book a ticket on Garuda's website, and I am Indonesian. They often have errors, etc. There are a number of possibilities:
1. What they call 'Sales Promotions' are usually still more expensive than other LC Carriers. Did you look at the 'total price' left hand side? Because the surcharges are often as expensive as the tickets.
2. Garuda has different prices. Special prices sometimes are only available for online purchases (with all the hassles and errors you get with it) ;-) So buying through an agent would give you a different price.
3. They have very limited seats. If when you book 4 seats, you get more expensive price than when you book 1 seat, that means they have fewer than 4 seats you just have to keep trying to get the best pricing combination.
4. I think they have a weird data mining method to determine pricing, or maybe none at all. Because Garuda don't have short time limits like LC Carriers, it's possible the tickets were booked by someone and not purchased, and then cancelled. So it doesn't reflect availability very well.
This is my view as a layman.