We have several domains with GoDaddy, all sharing the same IP address. We use CPanel email for all of the domains, except one, which has just recently been set up to use Office365. This works OK, except that emails originating from any of the other domains do not reach the new Office365 accounts. Email from other external sources works OK, implying that the MX record for the domain is set up correctly.
It appears that GoDaddy originated mail is not using the information in the MX record, but is going direct to the old email accounts.
Is there a way to stop this happening, so that our internal email will work as previously?
Not sure if you were able to work this out on your own already, but I think there may be some additional details missing that would allow other members to help with suggestions on how to resolve this.
Like for clarification, the messages you say you're not receiving are only the domains setup on cPanel mail to your Office 365 domain? Did any of the sending addresses you're having trouble receiving messages from indicate any sort of error or bounce back reply? I'm assuming you may have also checked your bulk messages folders to be sure the messages were not filtered by mistake.
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