@JBerns
The screencast link you sent didn't work, something about the video being "unlisted".
However, I managed to open your cad files (had to download a newer version of IV to do so), and I can't see Inventor allowing two iMates with different offset values to match (using the ALT-drag technique)
To be double sure, you should be able to create an iMate the same way as you would normally create a constraint, but instead of selecting geometry, select the iMates in the model browser.
In the assembly you sent, you will notice you can create an iMate between 'Align1' in both the bolt and the washer using this method, but its impossible to do the same with 'Insert In1' as the offset values don't match.
Here's a snip from the IV help that confirms this:
"The iMate definition properties must always match for the iMate definitions to match. iMate definitions with matching names and match lists, but without matching properties, do not match."
My guess is that when using the ALT-drag technique you are mistakenly picking up on a model edge rather than the other iMate.
I use fasteners from content center but I've never had to create iMates for them using code. I often constrain them manually then use Component.Replace if I need a different size & the constraints stay intact. What's your complete workflow? There may be a better way to achieve your end goal.