There could be many things causing that.
I can think of 3-4 reasons.
I can give solutions to them, try these if these don't work then i may need to inspect the image my self.
1st usb drive speed
If the drive is very old 6-8 years then, it could cause that, normally read speed above 8 MBps should boot under 1 min, if it boots fast in VM
so try other drive only if your drive is old.
2nd UEFI/secure boot there are many names to what MS did in its new booting mechanism.
But basically its a fast booting mechanism in windows 8 and higher OS, In which some part of OS is loaded in BIOS/ROM available in system to boot installed OS around 3 sec, So its basically a half pre-loaded installed os which is causing the problem, In multi-OS boot setup, if you boot OS other than default setup it takes minute or 2, in re-configuring that, you may have experienced it your self
so try any win 7 installed PC, or restart PC and at post (keep power button pressed for 8-9 sec) and then try.
3rd your source OS for PE may not be comparable.
Microsoft may have again modified booting mechanism.
In that case you know what to do.
4th file system of your pendrive
If you didn't formatted to active NTFS as i said early
If you did then try power iso's option write image to pendrive in options menu
It normally should be slower then default method, but it will give us idea about where are you mistaking.
There are few other things but you should try these, I think they should work if it boots fast in VM.
Edited by getnikkoo, 11 December 2017 - 07:26 PM.