It gets funnier: I changed the script now:

echo = co
  cvs -d ${REPOSITORY} co missing_commit
date +%s
  cd missing_commit
  echo "dead1" > file1
echo = ci
  cvs ci -m "dead1"

This is the output I get:

[…]
= co
cvs checkout: Updating missing_commit
U missing_commit/file1
{sleep:1311862405<1311862405=0}
{slept:1311862406<1311862405=-1}
1311862406
= ci
cvs commit: Examining .
= log
revision 1.2 not present in the log

This is the dates:

tg@zigo:~/X $ date -d @1311862406
Thu Jul 28 14:13:26 UTC 2011
tg@zigo:~/X $ stat working/missing_commit/file1
  File: `working/missing_commit/file1'
  Size: 6               Blocks: 8          IO Block: 4096   regular file
Device: ca00h/51712d    Inode: 667057      Links: 1
Access: (0644/-rw-r--r--)  Uid: ( 1000/      tg)   Gid: ( 1000/      tg)
Access: 2011-07-28 14:13:25.000000000 +0000
Modify: 2011-07-28 14:13:25.000000000 +0000
Change: 2011-07-28 14:13:25.000000000 +0000

WAAH?! Definitively not a bug in CVS.

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https://bugs.launchpad.net/bugs/12230

Title:
  cvs checkout is racy, it wasn't in the past

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