Premiere pro cc 2014 Rendered out video not matching sequence, as well as sequence constantly changing
I'd say you may need to do nested compositions; and pre-renders with that many layers. 

The honest truth is there are bugs in premiere... in terms of if you have a lot of layers; with specific opacity settings, or filters applied to them; in particular 3rd party filters; they simply don't always play well together. 

Thats why AfterEffects tends to be a more useful platform for projects using lots of layers. 

They are idiosynchosies... they don't make sense... in terms of what causes them. They might preview correct within premiere, but output with issues. 

The fix is typically to either move to AE, or pre-comp grouped layers to reduce the total layers/effects. Render pre-comps of layers with effects applied, then use the new file as the source with no filter. 

Lastly, as stated above, make sure you are interpolating your footage to the same standard, progressive or interlaced.