I had all te size and timeout limits set fine on my server (all the ones documented in the FAQ, anyways), but file uploads were still being limited to about 15MB. When I checked my server's log, I found that there's another way to limit file size uploads on Apache when using fcgid to load php, which is a very common server setup. In the file /etc/apache2/mods-available/fcgid.conf on Ubuntu 10.04 (or the equivalent location for other Linux servers), there might be a statement which reads:
MaxRequestLen 15728640
This limits any uploads to the specified number in bytes. Commenting out the line or changing it to a different value fixes the problem.
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