If you're using Advanced Sequencer in NINA, you can use the Smart Meridian Flip plugin. You can point it at the .mlm file that APCC recorded your meridian limits to. It will turn off tracking before reaching the limit and stay that way until the target transits the meridian and clears any east-side limits of your mount. The flip will then be done and imaging resumes.

What you're currently running into with the stock NINA meridian flip engine is that you probably have not specified a sufficient value for the Pause Before Meridian setting, so your mount is rolling up on to the limit and parking before NINA turns off the tracking.