Xts object comparison
This is not necessary related to xts. You are comparing to floating point values. As pointer out in this excellent resource these type of comparisons are dangerous. Best way to code it if you do not have Inf, -Inf or NaN is by doing,

(abs(rts.fut$Ret - rts.fut$Ret2) / pmin(abs(rts.fut$Ret) + abs(rts.fut$Ret2),
  .Machine$double.eps)) &lt; .Machine$double.eps


Hope this helps.