First off, I think the assigned slot values - especially top 5 - have included in them a built-in under-slot bias where a team not only benefits from picking early but is reasonably assured of saving some dollars to aid in signing others. Saving $100k on some 9th and 10th rounders is nice, but it doesn't add up quickly. Saving $1-2 million on an early pick gives a team lots of flexibility.
It looks like most of the signability issues are related to guys that are still being offered 7 figures. While this figure mist start with a "1" instead of a "2" or "3", these kids still need to weigh their options carefully. If they were thinking $1 million 6-8 months ago and just happened to start climbing since then, are they really going to pass on the $1 million.
Lastly, saw a comment here that one should go back and re-order the draft based on bonuses. Some folks think teams should pick the best available still on the board, however I think teams are much more strategic. If a SS on the best available and the team doesn't need another SS (3-4 good prospects down on the farm), then they might choose a player who is more economical. Odds are stacked against the vast majority of these kids making it to the MLB for any length of time, so the risk of picking the 8th best remaining available instead of best available - especially after the 2nd or 3rd rounds - is a minor risk IMO.
Still trying to figure out how the Red Sox are going to scrape up enough money to sign Groome. They didn't save a whole lot of bonus dollars on their #2 pick if memory serves.