I have the same problem (on 14.04)
Error-Message:
Expecting 1633 bytes, got 47 at -1 at /usr/share/perl5/X11/Auth.pm line 39.
Unexpected short read from authority file/home/tom/.Xauthority at 
/usr/share/perl5/X11/Protocol.pm line 2303.


xauth seems to work fine:
tom@aretha:~$ xauth -f .Xauthority 
Using authority file .Xauthority
xauth> info
Authority file:       .Xauthority
File new:             no
File locked:          no
Number of entries:    3
Changes honored:      yes
Changes made:         no
Current input:        (stdin):1
xauth> list
aretha/unix:1  MIT-MAGIC-COOKIE-1  8c47bb7e03b351bdbf498310cdcaf9fe
aretha/unix:10  MIT-MAGIC-COOKIE-1  383dd7755ff4c565bed25b57e67f31aa
aretha/unix:0  MIT-MAGIC-COOKIE-1  13f5fea5d7380359c173e8bc5c339494
xauth>

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https://bugs.launchpad.net/bugs/1393483

Title:
  error reading .Xauthority

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