I have the same problem, running on a KVM vm.
Is there no easy way just to zero negative values ?  

Do i understand the problem correctly that by the time the server
reboots, the clock has moved forward, and then during the reboot it is
reset (moving back in time) and then when the server comes up it logs
negative uptime ?

root:~# uprecords 
     #               Uptime | System                                     Boot up
----------------------------+---------------------------------------------------
->   1    12 days, 21:29:37 | Linux 3.13.0-24-generic   Tue May  6 10:04:07 2014
     2    12 days, 21:21:05 | Linux 3.13.0-24-generic   Tue May  6 10:03:42 2014
     3     9 days, 12:39:58 | Linux 3.13.0-23-generic   Wed Apr  9 12:44:30 2014
     4     8 days, 21:50:07 | Linux 3.13.0-23-generic   Sat Apr 19 01:25:08 2014
     5     6 days, 14:53:29 | Linux 3.13.0-20-generic   Wed Apr  2 21:50:35 2014
     6     5 days, 07:00:40 | Linux 3.13.0-24-generic   Sun Apr 27 23:16:57 2014
     7     3 days, 03:32:53 | Linux 3.13.0-24-generic   Sat May  3 06:29:28 2014
----------------------------+---------------------------------------------------
NewRec     0 days, 00:08:31 | since                     Mon May 19 07:25:11 2014
    up    59 days, 06:47:49 | since                     Wed Apr  2 21:50:35 2014
  down   -12 days, -21:-04: | since                     Wed Apr  2 21:50:35 2014
   %up              127.752 | since                     Wed Apr  2 21:50:35 2014
root:~# 

root:~# apt-cache policy uptimed
uptimed:
  Installed: 1:0.3.17-4
  Candidate: 1:0.3.17-4
  Version table:
 *** 1:0.3.17-4 0

root:~# lsb_release -rd
Description:    Ubuntu 14.04 LTS
Release:        14.04

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https://bugs.launchpad.net/bugs/498439

Title:
  uprecords reports >100% uptime

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