the only one i've seen where there were time intervals not a multiple of 5 was some boxer v yellow game. i checked to see if it was something that had to do with pre-1.10 replays vs. 1.10 replays, and it's somewhat true.
1.08 replays (not sure about 1.08b or whatever) have all sorts of time intervals (not just multiples of 5) where as 1.09 replays and on are only multiples of 5.
the only thing i can think of to rationalize this is that blizzard turned down the intervals at which players actions are recorded to slim down the file size of replays. seems kinda pointless and far fetched since replays were never really 'big' to begin with, but that's all i can think of.
so i guess the bottom line is that if you're going to compare replays with superview make sure that at any time you're only comparing 1.08 replays or post-1.08 replays.