For many of my web projects, I end up creating custom non-standard sized videos that are delivered as Flash video.

I would like to be able to archive the asset files in the final resolution, and I was hoping that one of the Cineform products would support this. For example the display size of the finished video might be somthing like : 426x240, 624x352, 800x400

I tried to do this with NEO SCENE, but the Cineform CODEC would not allow these odd sizes.

Any advice?

Two of those sizes work fine 800x400 and 624x352. The codec is limited to a width divisible by 16, but any height is allowed. That rules out 426x240, but 416x234 or 432x243 works. Divisible by 16 is extremely common size, as all distribution codecs are DCT based, which are optimized for 8x8, and for 4:2:0 16x16 block sizes. If you using some not with these sizes you are not encoding your distribution as efficiently as you could. We don't see adding any width support in the near future.

My your issue is something else. We did have an issue decode tiny images with low data rates in codecs before 6.2.1. This is a very recent change -- the beta for Neo v5.0 includes this new codec. I have tested down to 160x80 images -- the reverse direction that we are normally testing.