Pixel Bender runs in the same engine between the Toolkit, AE and PS. The only difference between them is the host application code itself. I need to look further, but the one thing I notice definitely missing is the Region Reasoning functions, specifically Needed and Changed (since you are doing some convolutions). In the Toolkit and PS plug-in, we use those region reasoning functions locally to improve performance. in After Effects, those functions are used as part of a much larger region reasoning pass. I'd start with those and see if that makes any changes.
See section 4 (starting p. 43) in the Pixel Bender developer's guide that is supplied with Pixel Bender SDK or downloadable from http://www.adobe.com/devnet/pixelbender/
If I get some time later, I take a further look.
Pixel Bender and After Effects act totally oddly. I really don't get it.
I have been trying the following lately:
define two parameters float3x3 to replace the constant matrices in the edgeX and edgeY functions by two dynamic ones. They are not editable in after effects but behave differently from the constantly defined matrices although they have the same values. With two (uneditable) parameters I can see some effect in AE that is different from the one in Pixel Bender IDE but at least there is something happening. I get completely white frames which I can turn into something visible by turning down the parameters Bias (to zero) and Factor (to something less than five or so). With constantly defined matrices inside the functions edgeX and edgeY nothing happens. The image simply stays black.
Where is the difference between a parameter float3x3 and a local variable float3x3 with absolutely and definitely the same values? And why does AE act differently from Pixel Bender IDE?
I also have been playing around with region reasoning functions needed and changed but I can't by the life of me get any results by altering them. Not even any negative results. They seemingly do nothing.
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now I'm thinking that this could be a difference between how the Toolkit and AE initialize parameters. I've sent mail to the engineer on the AE team that handles PB to see what he thinks and he or I will respond to this message.