Just thought I'd post an update. I've introduced controller heat calculations in my simulator that takes into account the major sources of heat including freewheeling losses, switching losses and mosfet resistance losses. Those details are provided in the text box after calculation, so if you're technically inclined, you can modify some of the parameters to make a more intelligible estimate. (Like, say, you think the switching time is more like 500 nS instead of 1000 nS, in both directions. Then you'd half your switching losses.)
The link is in my signature below. It also includes custom phase current limiting, so you can see how that may affect controller heat losses.
Anyways... it seems pretty illuminating now. At super low throttles, the "steady speed" makes minimal controller heat but slowing down by say, 2 mph, while only putting out 150 watts through the motor, may substantially increase the controller heat by a factor of 6-10x. So, a small variation in speed over variable terrain may explain why controllers get hot at super low throttle. I'll try to graph John's case to see what his actual numbers may be.
If anyone wants to correct me...
controller resistance = .006 (6 mOhm - pretend mosfets are hot.)
phase current limit = unlimited
battery current limit = 100 amps
a 5302 motor... ???
100 Volts battery
.1 Ohm battery resistance
20 inch wheel
Those are the big ones, I think...
Here's a sample picture.
This is at 7% throttle. At the "final speed" of 6.3 mph at 7% throttle, the controller is putting out around 29 watts of heat. However, if he hits a rock or hits a hole or bump or whatever while the motor is only putting out 150 watts of motor power, then it seems pretty likely that his speed may decrease by 2 - 3 mph. Looking at the graph, you'll see that the controller is putting out ~110 watts of heat in that situation if the bike slows to 4 mph for a moment.
Plugging in 25 volts into the simulator, it appears a lower voltage battery would help but not significantly (Though, if the controller has a thermal resistance of 2C/W, it'll be significant). We're talking about a peak controller heat wattage of 70 watts instead of 110 if slowed down by 2 mph from the steady-state speed of 6-7 mph.
Throttle pulsing or suddenly increasing the throttle from 7%-15% for a split second would certainly compound the problem. And, the thing is, the difference between 7%-15% is probably not noticeable to someone going over bumpy terrain (It's probably not even controllable).
Btw, when john opens up WOT at 7 mph or so, it appears the controller is instantaneously putting out ~1100 watts assuming no phase limit.

If the controller is relatively cool, that may be ok, but it would obviously be a problem at high controller temps. If he were to accurately limit the phase currents to 150 amps, it looks like the controller would be putting out about ~400 and would probably be more likely to survive. At 100 phase amps, it peaks at about 260 watts. A 5302 would have relatively sucky torque at those phase amps. It'd probably be better to move up to a higher winding - that'd reduce the strain on the controller, too.