(NOTE: This was solved, see http://www.sublimetext.com/forum/viewtopic.php?f=2&t=14417&start=20#p54868
So jon told me I was rude and basically implied I was a liar because he had never seen slow speed on win64. Maybe my posts were getting a bit angry, but after weeks with no replies as a paying customer, I am starting to get really frustrated. ST3 solves important problems for me, so it's a shame it doesn't actually work on my project...
So I'll try to explain my setup.
First of all, it's important to realize I use the EXACT same project on ST2 on the same machine with no problems whatsoever. Moreover, I use the exact same project on ST3 on a Linux machine with no problems whatsoever.
Recent ST3 builds on Windows 8 64 bit, however, is useless for me.
Project: 80,000 files, a few hundred of these are massive sql scripts. The project opens fine, but after a while, ST3 is unresponsive. The weird thing is that indexing/ST processes appear to be sleeping. Some sort of deadlock involved?
If there are some logs or something like that is available, I am happy to post these.
IIRC, the problem was introduced in build 3019 from March, but I'm not 100% sure.