The AE2 inscriber machine will only work when a single item is in any of its slots. A normal hopper will only put in 1 item at a time. The Logistical Transporters/Sorter will force stacks of items into this machine, causing it to no longer function.

Is it possible to put more-than-one-item stacks into the inscriber by normal means (clicking it in there from your inventory)?

No. It is not possible to put in more than one from your inventory, nor will a hopper put in more than one item at a time.

Logistical Transporters also happen to have some odd interaction with MFR machines. First, it won't accept output from MFR machines, requiring a chest intermediary to get it to function. Also, it for some reason pipes items into the upgrade slot and forces a stack of items into that slot, despite being unable to manually place items (other than the actual upgrades) into that slot and when an ExtraUtils setup on the exact same side outputs to the inventory normally.

Huh, this is indeed strange. Looking for a fix...

Fixed. I wasn't checking for strict inventory stack limits.