Wow, turn my head for a measley 6 hours and 30 minutes and WHAM !
First of all, thank you all for chiming in, more info always helps.
Secondly, the first thing that jumps out at me is that all your systems are ones that I can not recreate here (Lin and sometimes Win, but only 10.6 Snow Leopard for testing, well, you understand)
Os your using and the version of Lc.
mvillion - Mac Sierra 10.12.5. LC 8.1.5RC but it does not matter
Craig - LC 6.7.9 on Mac OS 10.9
@Craig, 2M/2400 control stacks? Dang, see me after school

(Just kidding, but no less it is impressive)
@mvillion, no 3rd party plugins actually benefits the testing process, so really helpful and easy to reproduce setup. I'd guess, though, that since 2 other people at least experience this issue, and both of them far more knowledgeable than I about Lc, that your first question
Has anyone else seen this?
is answered.
We are making
progress !
I am going to go out on a limb here, and say that since the Lc vers. doesn't seem to matter (at least down to 6.7.x), that it would be an ongoing thing, not something that just cropped up in the latest IDE builds. (Dazzling, aint it?)
richmond62's thought was valid about project complexity, however you have confirmed that this takes place with the same stack, and pointed out that it happens randomly regardless of the stack you are working on.
... I will take this to mean that even if you had a relatively simple project, one stack, one card, a few objects (say, 2 buttons, 2 fields, some labels), that you've seen this? Please point out if this assumption is invalid.
This leads to some more questions:
1. How much time is lapsing between the builds, i.e. are you changing one line/multiple lines, more than 1 minute, etc.
2. Are you saving the project before building each time?
3. Have you ever closed/re-opened the IDE after one of these events seems to start happeneing? Does that change the behavior back to building the standalone quickly? (less than 1 minute build time)
My (admittedly limited) understanding of the IDE is that the entire IDE + project are in memory, with the IDE performing all garbage removal/cleanup (correct me if my assessment is incorrect).
...I assume this includes things going on when building the standalone. As well, the IDE puts builds into new folders as you go (proj1, proj2, etc). I don't know how it handles that part of it, but that could be adding to the problem if it is just waiting to do clean up.
I have been saving build after build. Sometimes the process takes 20 seconds, sometimes four minutes. i do not believe that other processes on my Mac are significantly different from instance to instance.
I believe you are fundamentally correct, however depending on how the IDE is allocating/cleaning memory and how your os reacts to that, it could account for severe lag times in processes.
For instance, if the IDE is doing a large dump (2M/2400 controls!?!?) AND the os is doing background file maintenance, or some other memory related operation, I could certainly see a lag being induced.
Something that would be helpful is if you could leave the current system processes utility up while you are working in Lc. When you notice this behavior, take a look at which processes are hitting the cpu/memory/hd the hardest at that point. I think that would give us the best shot at figuring out what is going on.
Now going to run some really fast build tests and see if I can reproduce this on Linux...