Is it normal that they are just disabled for drag and drop, and not the Save to Laserfiche button? 

Also I have tried the same email in my VM that works on my local machine and it's still greyed out on drag and drop.

The same emails are being greyed out as to the ones that were fine to be omitted yesterday. It's a little strange that one email is greyed out in one system and not in the other yet the checkbox is allowed with the toolbar save button.

Edit3: Downgraded my VM and it's a 10.3.1 bug. Can't see what else it'd be.

In the case where it allows you to unselect the option, does the attachment actually get removed from the edoc that gets imported? You can tell by comparing the size in the document properties dialog:

in 10.1 dragging and dropping doesn't seem to be removing the attachment (although you can't see it and it's not in the repository anywhere which is good enough for me and the customer).

In 10.3 using the save to laserfiche toolbar button results in a much smaller file and seems to completely get rid of the attachment, but no drag and drop functionality. 

Should I make a support case to request this be looked at? It looks like the functionality of the way the email is brought in has changed, 

The drag and drop type is application/octet-stream whereas the save button is application type unknown. Possibly the way the attachment before 10.3.1 was just to hide it where in 10.3.1 it's actually stripping out the attachment properly but breaking on drag and drop as the import is different? Just a guess at the minute but as far I can tell I can't get anyway to strip the attachment when dragging and dropping emails but works much better using the save to laserfiche button 

I would have guessed the functionality would work that the drag and drop event kick off the same save to laserfiche dialogue but it seems like it works completely differently. 

I think the "Leave in message" functionality is largely ceremonial. Even when this is unchecked, the file size is not changed drastically. To be clear, I am talking about the attachments being left in the original MSG file in Laserfiche. I tried this on 10.2 and dragging a msg file with a 5MB attachment still results in a 4.77MB msg file in laserfiche. When i choose to leave the attachment in the message, the msg file is 4.82MB.

The file size isn't so much the issue, it's the fact there's an attachment now sitting in the repository for the customer. They aren't the most technically savvy and even having them navigate to the Save to Laserfiche button probably won't be a viable option.

I don't understand, are we talking about "Leave in message" or "Separate document"? The former is basically a useless checkbox, the latter controls whether a new document is created from the attachment. As far as I know, the "separate document" checkbox works correctly in all cases.

To add to what Robert said. Leave in Document and Separate Document are not one or the other toggles. You can do both, or (in cases where the attachments aren't embedded) neither. Just because the attachment is or isn't left in the document doesn't control if it is imported as a separate document.