Have Neo Scene for 5d, but 5d is sold and thinking about a T1i which is shooting 1080p at 20 fps and 720p at 30, do I foresee any Neo Scene problems, its still a mov. h264 clip

With the latest builds (123 and later for Neo Scene), it should not be a problem, assuming it's the same as the 7D files.
http://www.dvinfo.net/forum/cineform-software-showcase/462659-new-beta-builds-feature-canon-7d-support.html

the 30p should be no problem, the 20p 1080, should be ok assuming NEO will leave the original frame rate as is, just thought I might get Cineform to comment

Sorry! you are Cineform!