I never had this problem, so I can't tell how to get success with that. BUT: in older MLVApp versions (I think < v1.0) we had (under RAW Corrections) an option "Deflicker target". It accepts values from 0 to 9999, if I remember right. We don't know how to use it (that is why it is not there today), we just added the existing code to the app. Maybe we did not have the "correct" test footage for it. You could try with that. If that works... there is a hidden feature in the current MLVApp version: deflicker target is still there, it is just invisible (and untested, no idea if it really works). You can access it with the receipt and session files. These files are XML based. Search for the entry:
<deflickerTarget>0</deflickerTarget>
and change the number. Reload the file and have a look if something changes. As written... no idea if that helps... but maybe you have a try.
Edit: tried with some values... MLVApp accepts them (you'll see when exporting the receipt brings the values) but I don't see any effect on the footage - but I don't know what value has which effect. Maybe my input is just wrong.