HuffYUV problem and video encoding

I have a dilemma. Adobe Premiere CS6 or Adobe Media Encoder, do not support variable framerate. So now I have to convert my videos to a constant framerate without losing any quality.
I'm aware of Lagarith but nothing encodes to it. ALL of the encoders I mainly use support HuffYUV, and they encode it way faster than something like VirtualDub. It's many hours of video. I thought Adobe Media Encoder would solve it, but it turns out that didnt support converting variable framerate to constant. So my audio and video are out of sync in premiere.
I cant really get it into Lagarith so I probably just need to somehow use HuffYUV, anybody know of a HuffYUV plugin for premiere or something?

You shouldn't need a plug-in for that to work, as long as the codec in installed on the system.

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