I think I am experiencing something similar. I had issues when migrating from 5.6.3 to 6.0.2 because I was actually excluding default.css before. Once I removed that a lot of my issues were resolved.

Now after upgrading from 6.0.2 to 6.1.0 I see some similar issues. Like the Manage button is displaying at the top left on many pages instead of actually hovering above the module instance.

Any good way to work around this would be very helpful.

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Forerunner Communications, LLC
DotNetNuke Integration Specialists

Thanks for creating the ticket Robert. It took me about 3 weeks to iron out all the css, js, jquery issues on my site when moving to DNN 6.0.1 and I am hoping it won't take weeks to resolve this issue. I probably should have waited to do the upgrade but there was another issue introduced in DNN 6.0.1 that was being corrected in 6.1.0. So I wanted to do the upgrade ASAP. But if all else fails with this particular issue I do have a full set of backup files to do a restore until it is sorted out.

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Forerunner Communications, LLC
DotNetNuke Integration Specialists