Recently I used two MWS accounts from same server. And Amazon sent us an email that you are operating on two accounts.
Do they track IP's of API calls?
How can I use both accounts?
Are you using multiple developer credentials? In my case, as a developer, I have a set of developer credentials that I use for all my clients. I use the token and seller id that they provide me with. I service multiple clients on a web page using a single set of dev credentials, only swapping in/out the client token and ID.
Check out this FAQ for further info.