Output from "strace -f rpm -qa" (only few last lines)
I did "rm /var/lib/rpm/__db.001" before strace.

...
munmap(0xbf3ea000, 4096)                = 0
open("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/rpm.mo", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/share/locale/en_US.utf8/LC_MESSAGES/rpm.mo", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/share/locale/en_US/LC_MESSAGES/rpm.mo", O_RDONLY) = -1 ENOENT (No
such file or directory)
open("/usr/share/locale/en.UTF-8/LC_MESSAGES/rpm.mo", O_RDONLY) = -1 ENOENT (No
such file or directory)
open("/usr/share/locale/en.utf8/LC_MESSAGES/rpm.mo", O_RDONLY) = -1 ENOENT (No
such file or directory)
open("/usr/share/locale/en/LC_MESSAGES/rpm.mo", O_RDONLY) = -1 ENOENT (No such
file or directory)
stat64("/var/lib/rpm/DB_CONFIG", 0xbff053b0) = -1 ENOENT (No such file or directory)
open("/var/lib/rpm/DB_CONFIG", O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file
or directory)
stat64("/var/lib/rpm/__db.001", 0xbff053e0) = -1 ENOENT (No such file or directory)
open("/var/lib/rpm/__db.001", O_RDWR|O_CREAT|O_EXCL|O_DIRECT|O_LARGEFILE, 0644) = 3
fcntl64(3, F_SETFD, FD_CLOEXEC)         = 0
open("/var/lib/rpm/__db.001", O_RDWR|O_CREAT|O_DIRECT|O_LARGEFILE, 0644) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
_llseek(4, 0, [0], SEEK_END)            = 0
_llseek(4, 8192, [8192], SEEK_CUR)      = 0
write(4, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"..., 8192) = -1
EINVAL (Invalid argument)
open("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/share/locale/en_US.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/share/locale/en_US/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No
such file or directory)
open("/usr/share/locale/en.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No
such file or directory)
open("/usr/share/locale/en.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No
such file or directory)
open("/usr/share/locale/en/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such
file or directory)
write(2, "rpmdb: ", 7rpmdb: )                  = 7
write(2, "write: 0xbff033f0, 8192: Invalid"..., 41write: 0xbff033f0, 8192:
Invalid argument) = 41
write(2, "\n", 1
)                       = 1
close(4)                                = 0
close(3)                                = 0
write(2, "error: ", 7error: )                  = 7
write(2, "db4 error(22) from dbenv->open: "..., 49db4 error(22) from
dbenv->open: Invalid argument
) = 49
write(2, "error: ", 7error: )                  = 7
write(2, "cannot open Packages index using"..., 61cannot open Packages index
using db3 - Invalid argument (22)
) = 61
rt_sigprocmask(SIG_BLOCK, ~[RTMIN], [], 8) = 0
rt_sigaction(SIGHUP, {SIG_DFL}, NULL, 8) = 0
rt_sigaction(SIGINT, {SIG_DFL}, NULL, 8) = 0
rt_sigaction(SIGTERM, {SIG_DFL}, NULL, 8) = 0
rt_sigaction(SIGQUIT, {SIG_DFL}, NULL, 8) = 0
rt_sigaction(SIGPIPE, {SIG_DFL}, NULL, 8) = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
write(2, "error: ", 7error: )                  = 7
write(2, "cannot open Packages database in"..., 46cannot open Packages database
in /var/lib/rpm
) = 46
fstat64(1, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 7), ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) =
0xbf3ea000
write(1, "no packages\n", 12no packages
)           = 12
munmap(0xbf3ea000, 4096)                = 0
exit_group(1)                           = ?

Yup, kernel has new semantics for O_DIRECT thereby
breaking rpm.

Adding LD_ASSUME_KERNEL=2.2.5 should fix sufficiently
to upgrade to rpm-4.2-1 packages at
    ftp://ftp.rpm.org/pub/rpm/dist
which have better fix.

Add as prefix, like
    LD_ASSUME_KERNEL=2.2.5 rpm ...

i'm using arjan's new 2.6.0 test rpms on rh 9, and I see this problem.  I
originally saw it with rpm-4.2-0.69, so I read this bug and upgraded to 4.2-1
from ftp.rpm.org and I still see exactly the same behavior.

installing the new rpm package and rebooting fixes this bug for me.

Experienced the exact same problem here on a RH9 box with a homebrew 2.6.0-test2
kernel. Updating rpm with the rpm-4.2-1 packages from ftp.rpm.org fixed the
problem, but only after rebooting. Just upgrading rpm or even going singleuser
was not enough. Thanks for the fix!

I have the same problem here in a Shrike box with kernel 2.6.0-test3 (custom, I
had to recompile only to add support to i810 graphics in kernel and not as
module). I will try to upgrade RPM (hopefully from rawhide) to see if that fixes
the problem.

It did fix the problem.

I'm using kernel 2.6.0 with RH9 and this solution works perfectly.  I
wish I hadn't had to reboot though.... can someone figure out why it
requires a reboot?

Yes, This works.
Under my RH9 with kernel 2.6.4  rpm only works with no root user. 
Then like root and using LD_ASSUME_KERNEL parameter before rpm 
command works well. Remember, I just used this one time to upgrade my 
rpm for rpm-4.2.1 and then reboot machine.

roo# LD_ASSUME_KERNEL=2.2.5 rpm -UvH rpm-4.2.1-i386.rpm

Current RPM is FC2 is rpm-4.3.1-0.3. I assume this is fixed there too...