xts and Sys.time() - very stange behaviour

This is an issue with precision and formatting when you convert to
character.

<...>

I don't know of a solution, other than "don't do that".

I found that keeping the POSIXct object, and modifying that directly, 
massively improves both speed and correctness of matching over using the 
character representation with sub-second data.  This of course makes 
sense, as you are matching a number to a number, rather than a number to 
a string converted to a number.

Regards,

    - Brian