Hi Alice,
My company had a similar issue since integrating Dynamics in January. I'm not sure of the issue entirely as I'm not in IT, but Dynamics was overwriting a large number of global contacts in our Marketo instance with the wrong company name completely.
The solution we came up with was to change all the company name fields that were affected back to "Unknown" so customers weren't seeing the wrong information and create a new company name field in Marketo and map Dynamics to it. So far with using the new company field we haven't seen the issue again.
The downside from my perspective is having to update all our existing forms in Marketo to use the new company name field. Because we're a global company, have reporting restrictions and divide our Marketo instance into regional workspaces, there's about 2,000 live forms to update. We hired a local Marketo vendor in Portland, Lead Lizard, to assist with creating a solution and help update the forms.
If you can't get assistance from Marketo Support, I'd recommend reaching out to Lead Lizard and ask for some assistance. We had the problem solved and solution in place within a week.
Jamye