unexpected subsetting behavior after gathering with tidyr

What's going on here?

Setup

Create y1 and y2 , equivalent data.frames. y1 is generated using gather and y2 is read in directly.

library(tidyr)
x <- data.frame(id = 1:2,
                 day_01 = as.POSIXct(c('2015-03-09', '1989-02-11')),
                 day_02 = as.POSIXct(c('1985-09-11', '2000-08-15')),
                 gender = factor(c("M", "F")))
y1 <- gather(x, key, value, day_01, day_02)

y2 <- read.table(text="id gender    key      value
 1      M day_01 2015-03-09
 2      F day_01 1989-02-11
 1      M day_02 1985-09-11
 2      F day_02 2000-08-15", header=TRUE)
y2 <- within(y2, value<-as.POSIXct(as.character(value)))

y1 and y2 are equal

all.equal(y1, y2)
# [1] TRUE

Problem

Subsetting y1 drops the POSIXct column to numeric, but subsetting y2 in the same way does not.

y1[y1$gender == 'M', ]
#   id gender    key     value
# 1  1      M day_01 1.426e+09
# 3  1      M day_02 4.953e+08

y2[y2$gender == 'M', ]
#  id gender    key      value
#1  1      M day_01 2015-03-09
#3  1      M day_02 1985-09-11

Session info

R version 3.1.2 (2014-10-31) Platform: i386-w64-mingw32/i386 (32-bit)

tidyr 0.2.0.9000

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