Will ms brain lesions show up on an mri as well when not having a "flare up" or are they seen more easily during flare up?

Can be seen: The MS plaques can be seen with or without a flare up. Active plaques may be seen with contrast.

MRI changes: MRI changes can be seen in the setting of MS even when there are no clinical symptoms. This is why the MRI is helped to make the diagnosis. Not all flares cause clinical symptoms, but when there is a flare, there is normally a change seen on the MRI (either of the brain or the spinal cord).