But hold on, That adjustment should have nothing to do with tracks syncing up? And not only that, That is a preference stting and loading another project would not have changed your preferences. Maybe what was happening is you were recording while having input echo on so somehow playing along to latency, but that still is a bit confusing.
And the latency slider is not available in ASIO mode, You make that adjustment with your audio interface control panel, So something is still not set up right here. I think your using the wrong timing master , not in ASIO mode and your system has very noticeable latency which you are monitoring.