When applying time remapping on a cineform .avi in Premiere CS4 (on a PC) it's not rendering correctly and the timing is completely off. The same clip on the timeline was playing fine before it was rendered.

Work with support, there is no reason this shouldn't be working for you. If you are talking audio speed, that is a CS4 bug. Here is the simple workaround
http://www.dvinfo.net/forum/cineform-software-showcase/475244-cs4-cinverform-avi-export-audio-issues.html#post1507598