Using as.POSIXct in R giving na for identical character structures

It looks like a DST issue. I assume from your name you are from Sweden or thereabouts. There was no time in Sweden between 2am and 3am on the 31st March 2013, as the clocks went forward then.

as.POSIXct("2013-03-31 02:05:00",format="%Y-%m-%d %H:%M:%S", tz="Europe/Stockholm")
[1] NA

This is true for anyone on Central European Time (CET).