The problem is likely caused by phase problems with the lighting. Color stabilizer may help, roto probably will not.
As Rick said, the shutter phase and frequency wasn't synced to your lighting's electrical frequency, hence you have variations in there. You could try one of those flicker removla plug-ins like RevisionFX' DE:Flicker or the Beta of Digital Anarchy's Flicker Free. Otherwise doing it the hard way with AE's internal effects is certainly possible like using Auto-Levels to stabilize the luminance...
Dear Rick and Mylenium,
Thank you for your help. The Digital Anarchy's Flicker Free is amazing and works on my footage so well. That is save my life