[I caught some misconceptions here which I think will this post clear off eventually]
There should not be any difference since both refer to
/var/run/utmp file, which has its own format to store the records. If at all there is any difference, then your utmp file is busted. uptime shows the amount of time that has passed since the system has been booted or how long the system has been running. It does not tell you the system clock or system boot time . System boot time information is stored
[centos@centos temp]$ date; uptime; who -b
Fri Dec 9 20:41:40 IST 2011
20:41:40 up 1:32, 2 users, load average: 0.50, 0.37, 0.29
system boot 2011-12-09 19:11
uptime refers as well /proc/uptime, which essentially keeps the counters in kernel.
[centos@centos temp]$ sleep 1; cat /proc/uptime; uptime; sleep 5; cat /proc/uptime ; uptime
20:47:39 up 1:38, 2 users, load average: 0.29, 0.31, 0.27
20:47:44 up 1:38, 2 users, load average: 0.56, 0.36, 0.29
/var/run/wtmp is referred by last/lastb commands.
last reboot will show a log of all reboots since the log file was created.
Additionally, if you are having /proc filesystem, then tool such as
procinfo can give you bootup time as well.
bash$ procinfo | grep Bootup
Bootup: Wed Mar 21 15:15:50 2001 Load average: 0.04 0.21 0.34 3/47 6829