If I remember correctly, there is a certain "allowance" on the rune cooldowns that allow you to be late when using a rune and still get the rune to cooldown as if you used if exactly when it became available. I believe this is a 2 second allowance.
So you use a rune and it goes on cooldown. 10 seconds later, it becomes available. If you use it exactly as it comes off cooldown, it goes on a 10 second cooldown again. If you use it 1 second after it becomes available, it goes on a 9 second cooldown, because it's treated as if you had used it exactly when it comes becomes available. Essentially this means that the rune will be available again 10 seconds from when it last became available. If you use it 2 seconds "late", it goes on an 8 second cooldown. Anything later than 2 seconds will still incur the 8 second cooldown.
So what you were experiencing was probably this:
Your death runes come off cooldown (for Obliterate). A few seconds later, you see that your frost fever has 10-10.5 seconds left just as you use Obliterate. 8-9 seconds later, your blood runes come off cooldown earlier than you expected, because they benefited from the 2 second "allowance".