I'm running RedHat Enterprise 6.2(Linux version 2.6.32-220.el6.x86_64 (mockbuild@x86-004.build.bos.redhat.com) with Dual Intel Xeon Processor(L5638) configuration.

When I used RedHat 5.x version with this system, "CPU: Physical Processor ID" appeared exact number of cores on the server. For example, this L5638 has 6 cores and if I enabled HyperThread on the BIOS, this "CPU: Physical Processor ID" showed 24 times in the /var/log/dmesg file.

After upgrading(actually installing) from RedHat 5.x to RedHat 6.2, this "CPU: Physical Processor ID" showed only one time and the value of this are not fixed. Followings are case what I got.

Case 1)

Initializing cgroup subsys perf_event
CPU: Physical Processor ID: 1
CPU: Processor Core ID: 0
mce: CPU supports 9 MCE banks
CPU0: Thermal monitoring enabled (TM1)
using mwait in idle threads.
ACPI: Core revision 20090903
ftrace: converting mcount calls to 0f 1f 44 00 00
ftrace: allocating 20776 entries in 82 pages
Setting APIC routing to physical flat
..TIMER: vector=0x30 apic1=0 pin1=2 apic2=-1 pin2=-1

Case 2)
Initializing cgroup subsys ns
Initializing cgroup subsys cpuacct
Initializing cgroup subsys memory
Initializing cgroup subsys devices
Initializing cgroup subsys freezer
Initializing cgroup subsys net_cls
Initializing cgroup subsys blkio
Initializing cgroup subsys perf_event
CPU: Physical Processor ID: 0
CPU: Processor Core ID: 0
mce: CPU supports 9 MCE banks
CPU0: Thermal monitoring enabled (TM1)
using mwait in idle threads.
ACPI: Core revision 20090903
ftrace: converting mcount calls to 0f 1f 44 00 00

As you saw, the value in "CPU: Physical Processor ID" are not identical even though I didn't change any configuration from hardware and software point of view.

Does anyone have idea when this "CPU: Physical Processor ID" has 0 and when this has 1?

That is kind of strange, but the processor ID should always remain the same. If you have two processors, then you should always see a zero and a one. Try running this and see if anything changes:

That's what I expected. I took logs twices as I mentioned it showed only single physical processor and ID is changing when I rebooted

$ ls
dmesg_ht_0 dmesg_ht_1
$ grep "Physical Processor ID" *
dmesg_ht_0:CPU: Physical Processor ID: 0
dmesg_ht_1:CPU: Physical Processor ID: 1

These logs were taken on the same machine.