Julia
There's nothing worse that strange Eloqua behaviour and then trying to figure it all out. I guess if you got error messages on upload you would have mentioned it. And once uploaded, does the upload report look OK? Not my area of specialty but has a customer admin taken a look at the upload history?
A way to test if integration is an issue here is to see if a: you can manually change a record in Eloqua (not by uploading but editing the contact record. If you can make and save the change, does that 'stick' or is it later overwritten via integration? If it sticks the issue is not integration, it's the upload.
I would re reluctant to make any changes to the integration rules, they are there (or should be there) for good reason. The alternative would be to consider making the contact updates in your CRM and not in Eloqua.
Greg