Actually, in the light of this:
>> I sent myself a company PDF to my personal email. It opened with no issues on my phone/aquamail.
>> i resent the same email to my work address, and it would not open on my phone/aquamail, but it did open on my desktop.
I would ask for a different test.
1 - Enable debug logging with "raw data".
2 - Send yourself a PDF from web mail or desktop (to keep Aqua's log less cluttered).
3 - Check mail in first account (just the account, or the folder would be even better, to reduce the clutter), wait for test message to show, click the attachment so it downloads too.
4 - Same with the second account.
I think we're going to find that it's a server bug (specific to IMAP, and how AquaMail fetches attachments separately from message text -- as opposed to fetching complete message and breaking it into text + attachments in the app, like K9 Mail does...)