Differences of seconds (or even tens of seconds) should not be surprising. "Current Time" corresponds to what the user perceives from the clock displayed. If you watch the displayed clock, it will not always change immediately. Read the docs:
http://developer.android.com/reference/android/os/SystemClock.html
It's pretty clear that you can't depend on currentTimeMillis
for much of anything where you need millisecond accuracy. However, in most applications you really don't need that level of accuracy...
If you are trying to determine "exact boot time" from a specific moment in time later, a few seconds probably is the best you will do. Besides, what qualifies as "booted"?? When the kernel is loaded? When the user can interact with the device? When the device screen lights up? When the device can actually be unlocked?
You should probably just listen for RECEIVE_BOOT_COMPLETED (Android - Start service on boot).
Here is the Android doc: http://developer.android.com/reference/android/Manifest.permission.html#RECEIVE_BOOT_COMPLETED