I use pwauth the following advanced options:

<securityRealm class="hudson.plugins.pwauth.PWauthSecurityRealm" plugin="pwauth@0.4">
<pwauthPath>/var/lib/jenkins/bin/stm-ad-auth</pwauthPath>
<whitelist></whitelist>
<enableParamAuth>false</enableParamAuth>
<idPath>/usr/bin/id</idPath>
<groupsPath>/var/lib/jenkins/bin/stm-ad-group</groupsPath>
<catPath>/bin/cat</catPath>
<grepPath>/bin/grep</grepPath>
</securityRealm>

Wehen upgrading jenkins to version 1.504, upon restart it tries to use the default:
...
Caused by: java.io.IOException: Cannot run program "/usr/local/bin/pwauth": error=2, No such file or directory

I got around this by symlinking to my pwauth and then re-applying the advanced settings with my custom paths. Can you make sure that these values are used right at startup instead?