This problem is a nightmare to diagnose, and worse to resolve!
A disclaimer is typically appended to emails by a program or appliance. However, corporate email also typically goes through anti-spam and anti-virus programs. There is also a difference between the way email is formatted if you use a Web interface instead of an email client - as in Outlook Web Access vs. Outlook.
At my company we ran into a problem where emails originating from Outlook, and then replied to in OWA, and subsequently replied to from a BlackBerry were getting their character set changed to an Asian Language character set so the BlackBerry reply was showing up as all Asian Characters! Given the unusual sequence needed to cause the problem, it wasn't showing up often and took about two months to figure out the sequence. Then the fun began! We have three separate "gateways" that email goes through - anti-virus, anti-spam, disclosure. Well it took another two months to figure out that it was the disclosure appliance which was altering the character encoding!
I don't really have any advice to give, but hope that story gives you some guidance on where to look!