Thanks, I finally managed to edit e1m1 as a test and it works. Indeed I had to switch to BSP-Win32 (I didn't even know these options before on Doom Builder) and without this option I had very slow or freezing speed and mistakes like passing through some sectors. Now, I noticed something that may or may not be related with your problems of things turning very slow when monsters wake up. There are two options in DoomBuilder, "BSP-Win32-Normal" and "BSP-Win32-Fast (No Reject)". I tried the Normal so far.
From what I read here: http://doom.wikia.com/wiki/Reject
, the Reject table is something that speeds up monster check for seeing the player. This seems very relevant to your test, only when the monsters wake up and have to check for visibility of the player it goes very slow. Maybe you build with fast option? I will also check putting some monsters and building without reject table to see if there is a difference.
p.s. As an irrelevant note, I do remember now there was this reject table and few clever WADs were hacking it somehow, so they made a sector in the floor with pentagram shape where the player can go and suddenly the monsters will ignore the player and not shoot even if naturally he was in sight, like it's some magic pentagram of protection. There are so much happening behind Doom I still discover.