In this particular case, Steve apologized on air later for the "technical difficulties/audio problems". WFAN's default position when they have technical failures is to run spots until the problem is cleared up; this more often than not usually occurs on remote broadcasts.
As has been mentioned in previous threads about the CBS Sports Radio Network, the spot load on WFAN seemingly has increased since that network launched in January 2013. The spot breaks used to be about 4 minutes in length; they now usually run 5-7 minutes. And there are occasions where if an interview runs long (especially on Francesa's show), they'll double up on the spots to account for the ones that were "missed".
There's a couple of possibilities for the longer breaks:
1) WFAN is taking on extra ads that are tied into the sports network (such as with the network sports commentaries that air from 6am-6pm). This is although the network also runs ads on its over the air outlet in New York: the relatively unknown WCBS-HD2-101.1 signal.
2) Since about January, WFAN has clustered their spots a little bit differently than in the past. Before, they'd play about 3-4 minutes of spots leading up to a 20/20 sports flash, then about 3-4 minutes of spots after the flash. Nowadays, they'll usually play 6-8 minutes of spots leading into an update and then "go live" immediately afterwards.
I say "usually" with all these scenarios since their spot schedule varies with the amount and timing of guest appearances and topic discussions that run outside of the regularly scheduled breaks. There's definitely more flexibility on WFAN than there is on WEPN/ESPN Radio where they pretty much stick to the schedule of usually 10-11 minutes "live" followed by 4-5 minutes of spots/SportsCenter updates.
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With regard to Stern, his spot breaks over the last 5-10 years he was on K-Rock would usually expand to 13-16 minutes - this was done to satisfy Stern's desire to "get a flow going" with discussions/interviews, etc. I believe that at its peak the Stern Show was running up to about 24 minutes of spots per hour, which was one of the reasons he went past 10am ET: just to get in the extra minutes of spot time he didn't get in during the earlier parts of his show. (Imus was known to do the same when he was on WFAN - not sure about his show on WABC.) Other reasons why Stern "went long": 1) because he could - 2) because he was likely encouraged by management - 3) because it added ratings shares to the midday daypart in addition to the morning daypart. It's no wonder that WXRK NYC was billing over $50 million per year in its heyday.
This would lead to problems with some of the syndicated affiliates that didn't have enough inventory to fill out the commercial breaks: some would have their own traffic/weather/sports people to fill up time, which would annoy Stern if he found out about it - he'd tell them to "just run the show - don't add anyone or anything to it".
During Stern's vacation time when "The Best Of Stern" would run, management's (likely) preferred style of taking breaks would take effect: usually 3 breaks an hour of about 8 minutes apiece (unless it would really interrupt the flow of a recorded bit or interview, although they weren't afraid of breaking segments into Part 1/Part 2, etc.).