I have never heard of such a conflict.
What do you mean it "went down"? on your main website?
If you think there is a conflict, try testing a page w/o munchkin and a page w/o GA.
Agree with Josh. There's not enough information in your post, and there's no known conflict between the two -- quite the opposite, as most sites use both, Munchkin for named leads and GA more for anonymous/trending traffic.
If your IT guy can get a Community account s/he should probably post about it here with details.
They track behavior in slightly different ways, so metrics may not track perfectly, but it could also be due to partial loading, or incomplete tracking requests. Make sure your code is set up as detailed here to ensure the best possible data integrity: Lead Tracking (Munchkin) » Marketo Developers