Run 'postconf | grep size' and verify that the size limit is changing when you restart postfix--if not, then you have some really weird problem that's beyond my ability to troubleshoot, and may want to look at least at upgrading to a newer version and seeing if the problem persists. You also might not be using the standing configuration files
I see nothing wrong with the master.cf posted above, but I don't do local delivery on my box, so I might be missing something; one thing springs to mind, what's your mailbox_size_limit?
Add some context to the log file excepts you posted--what else is going on here?
Here's what I've done to try to replicate your problem:
Postfix 2.1.5 on RHEL4 (centos4, actually.)
message_size_limit set to 10000000
Server is a relay that forwards to an exchange box (with 10000000 msg size limit)
Generated 20MB test file (dd if=/dev/urandom of=/tmp/rand.out count=40960)
MMencode file (file size now 28350390 bytes)
Using elm as MUA. Attempt to send message:
Jun 15 18:21:13 smtp postfix/postdrop[3425]: warning: uid=0: File too large
Jun 15 14:21:13 smtp postfix/sendmail[3424]: fatal: root(0): Message file too big
Adjust message_size_limit to 50MB, and reload postfix configuration. Attempt to send message:
Jun 15 14:23:24 smtp postfix/pickup[3436]: 3AF389A821: uid=0 from=<root>
Jun 15 14:23:24 smtp postfix/cleanup[3446]: 3AF389A821: message-id=<20050615182324.3AF389A821@smtp.xxxxxxxxx.com>
Jun 15 14:23:24 smtp postfix/qmgr[3437]: 3AF389A821: from=<root@xxxxxxxx.com>, size=28739604, nrcpt=1 (queue active)
Jun 15 14:23:24 smtp postfix/smtp[3449]: 3AF389A821: to=<xxxxxxxx@xxxxxxxx.com>, relay=172.17.0.21[172.17.0.21], delay=0, status=bounced (message size 28739604 exceeds size limit 12288000 of server 172.17.0.21[172.17.0.21])
Jun 15 14:23:24 smtp postfix/qmgr[3437]: 3AF389A821: removed
Looks familiar, doesn't it? The difference is, of course, that the MTA that's bouncing my mail is on a remote machine instead of localhost, but the error is the same. Also note that the log excerpt above where postfix's limit is exceeded is a very simple 'fatal: message to big' instead of something bouncing from a relay.
I'm still thinking the problem isn't postfix.