My system clock runs a little bit too slow. I have no idea, what the problem cause might be. The problem did not occur with my old kernel 2.6.10. I do not know, what exact version introduced this bug.

Linux stefanspc 2.6.18-4-amd64 #1 SMP Thu May 10 01:01:58 UTC 2007 x86_64 GNU/Linux
stefanspc:~# cat /proc/cpuinfo
processor       : 0
vendor_id       : AuthenticAMD
cpu family      : 15
model           : 4
model name      : AMD Athlon(tm) 64 Processor 3000+
stepping        : 8
cpu MHz         : 800.000
cache size      : 1024 KB
fpu             : yes
fpu_exception   : yes
cpuid level     : 1
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow up
bogomips        : 1597.06
TLB size        : 1024 4K pages
clflush size    : 64
cache_alignment : 64
address sizes   : 40 bits physical, 48 bits virtual
power management: ts fid vid ttp

stefanspc:~# dmesg | grep tim
time.c: Using 3.579545 MHz WALL PM GTOD PIT/TSC timer.
time.c: Detected 1794.962 MHz processor.
Calibrating delay using timer specific routine.. 3593.39 BogoMIPS (lpj=7186780)
Using local APIC timer interrupts.
Detected 12.465 MHz APIC timer.
PCI: Setting latency timer of device 0000:00:01.0 to 64
PCI: Setting latency timer of device 0000:00:0b.0 to 64
PCI: Setting latency timer of device 0000:00:0b.1 to 64
PCI: Setting latency timer of device 0000:00:11.6 to 64
PCI: Setting latency timer of device 0000:00:11.5 to 64
Your time source seems to be instable or some driver is hogging interupts
stefanspc:~#