Unfortunately, no single test can rule MS in or out. It's more of a "big picture" diagnosis that takes things like lab tests, patient history, neurological exams, etc. into account. While nothing is 100%, it's much more common than not for MRIs to produce findings associated with conditions like MS. But, how your doctor phrased it is concerning. Clean MRIs do not, in and of themselves, rule out MS.
What you describe sounds a little too fleeting to be consistent with MS, though we're not doctors here. Because MS involves nervous system damage, things don't really resolve based on body position. Has your neurologist done a basic neurological exam? This doesn't involve fancy equipment and can still give them a lot of useful information.