So I installed a new shimano M443 crankset into a Miyata triple-cross frame, but the crank arms don't seem to be centered. The left arm is about 1/4" closer to the chainstay than the right arm. The frame was checked with an alignment tool and it isn't bent.

The bottom bracket that was included with the crankset was Shimano's ES25 octalink, for E-type derailers (68x121). It came with a 2.5mm spacer that I placed on the drive-side threads in place of the E-type hanger that wouldn't be present (I assumed this was what the spacer was for).

My question is, is this large of a difference in clearances normal? Should the spacer go on the left side? My caad9-5's crankset is perfectly centered, but my roommate's trek 7.2fx is offset about 1/8" in the opposite direction.

Remove the spacer would have been my first recommendation, but you should probably check the chain line.

You can eyeball it pretty easily-
Shift to the middle ring-
If an odd number of cogs in the rear, the middle one should line up exactly for a "straight" chain. Shifting to each adjacent cog should show the chain runing at a slight angle. These angles should be the same amount, but opposite side.
IF an even number of cogs, eliminate the "middle cog" from the above step and use the 2 "most middle" cogs.
IF it looks like you'd have a better chain line by removing the spacer, remove it.

They also make thinner spacers for this.

I honestly don't know, I've seen (and ridden) worse, and I've seen (and ridden) better. My body don't seem to mind either way. As long as the chain line is OK I wouldn't worry about it.

Take out the spacer. That will bring the cranks to within 1mm of even by my calculations.
(You want the whole thing shifted over by 1/8" or 3.175mm. Taking out the shim does 2.5mm of it, leaving you with 0.675mm difference)

I'll try that later. The threading on the fixed side didn't look like it would be able to screw completely into the frame though. The threads stopped exactly a spacer-width (2.5mm) from the flange.

What I'm confused about is that the BB cartridge was made for e-type derailers. Doesn't this mean I *have* to use a spacer on the fixed side if I am not going to be using the derailer?

edit: I'll also double-check the chainline.

Not centered crank arms shouldn't hinder performance any, but it is probably just visually disconcerting.
As a matter of fact, Phil Wood bottom brackets can be adjusted 5 mm left and right to adjust chainline.

The spacer may be installed for chainline.

Whether or not you want the spacer or not may start holy wars about that elusive topic of "Q-factor"....

So I removed the spacer and as expected, the cartridge couldn't screw all the way into the frame. I left the spacer off anyway because I was able to screw it in about a 1/16" more, and helped center the arms more. It's only about 1/8" off now and I'm just going to live with it.

Still strange that the arms would be more centered without the spacer for this BB.

It doesn't seem strange at all if you think about it.
The entire crank/bb assembly is shifted 2.5MM to the left.
The left arm is that much further away from the stay and the right arm is that much closer to that stay. Basically it makes 5MM difference in the before/after difference.

How's the chain line? That's what I would have used.
As I mentioned, they make thinner spacers, so if you feel the need to "fill the gap"....
https://www.loosescrews.com/index.cgi...d=440141517497

The proper way to check chainline is from the side of the seat tube to the tip of a tooth on the middle ring, then add half the ST diameter. The normal chainline for a Shimano road triple is 45mm and an MTB model is 50mm.

If there is a spacer provided, it goes on the right side, to make room for the third chainring.

Some crankarms may be offset by a few millimeters. A better way to check that is to rotate the arms parallel to the downtube and check the distance from the downtube for each one.

This is pretty common in my experience. Never had any physiological issues because of it.

If you had a non E type bottom bracket it would screw all the way in.