I've forgotten about this posting, until today when I got an email update.
After a lot of experimentation, we found out that the Intel WiFi management software needs Microsoft's wireless zero configuration service (ZCfgSvc,exe) to be running so that it can stop it and continue its own initialization. We have ZCfgSvc.exe disabled in our systems for some other reason. It seems like the Intel software is checking ZCfgSvc.exe status and expects it have been started and eventually times out doing so. This caused the 3 minute delay. So we just have to put ZCfgSvc.exe on automatic and let Intel's software disable it and this cut down the boot up times to less than 1 minute. Hope this helps