This may simply be a situation where a mod is set up to take unused cycles for some purpose - e.g. the wireless redstone mod may take unused cycles to listen for wireless transmissions in realtime (rather than processing a transmission queue whenever it has priority). It's difficult to know for certain without knowing a mod's implementation details, but it's not an uncommon practice in other server applications (non-Minecraft related).
In a similar vein, modtiming may be reporting idle time as belonging to the last mod active to forcibly display 100% utilization -- when it really ought to be reporting idle time separately. This would be a 'bug' (rather, an unimplemented but necessary feature) within modtiming itself.
It would be helpful if people could post their logs if they're seeing bizarre results from modtiming so that we can get a better idea of what's going on.