It's a dynamic situation with lots of reasons. Consider this scenario..
Ride that previuosly did not have a FP line (and hence no place for a FP line to assemble) now has such a line. The first Mickey is outside the attraction causing people to queue up outside, spilling out into public walkways. They are getting in the way. The whole "Mickey tap" thing takes time and the FP line builds ever bigger......
Attraction CM outside of ride (Tony)
Attraction CM at boarding area (Tonya)
"Tonya, this is Tony. I'm outside here and this Fast Pass line is really building up. We need to do something to clear out this mess. The Fast Pass people are complaining that they are having to wait 20-30 minutes with their Fast Passes. That is way longer than before. We need to get these people moving faster or else this new system is going to get bad word of mouth reviews."
"OK Tony. I'll do what I can. Sir? Yes, you at the front of the Standby Line. Can you please hold up for a moment so I can get some of these Fast Pass people cleared out?"
Tonya then lets 100 Fast Pass people clear out while the Standby line stays stagnant for 10-15 minutes not moving an inch. Then, in order to avoid another backup, Tonya increases the ratio of FP people to SB people such that the FP line boards at a brisk pace but the SB line moves at a crawl.
Remember. Disney was disappointed with the number of FP- that each person was averaging, (1.5 or so). It now gives you 3 and people are using them. There are twice as many people with Fast Passes walking around cutting off the Standby Lines. And to push this "benefit" even further, they have upper the percentage of ride capacity devoted to FP. So there may actually be three times as many Fast Passes cutting off the Standby lines. And Fast Passes are being used from the moment the parks open because when booking on line in advance, all times are viable. It used to be that 9:00-10:00 wasn't really a viable FP time. People didn't really want those times and you physically had to pull a FP the minute the park opened to get one of those early times. As soon as the clock ticked over to 9:15, those early FP times were gone for good. And when the clock ticked over to 9:30, more return times disappeared for good. In essence, there was a brief 30 minute window in which to book early FPs. Now, that window is 60 days plus 30 minutes. And with greater competition for FPs, people are booking those times. "Honey....the computer is telling me that the only time available for a Pooh FP+ is 9:15-10:15. Should I grab it?" And when FP people start cutting off the SB line starting at 9:05 and continue to pour in at a steady rate all morning long, the SB line starts to bog down early and only gets worse as the day progresses. We've gone from a system where the number of FP people getting in line at HM at 9:15 was zero to a system where that number is not large, but not insignificant. We've gone from a system where the number of FP returnees at Space Mountain at 9:15 was "dribs and drabs" to a system where that number is a steady stream. All of these FP returnees has to causes the SB lines to bog down.