HI folks and firstly thanks for the replies! OK so I should say we have implemented some changes which have resolved this issue in our install. I am not entirely sure anymore if this is a bug or a problem with OTRS, rather I am starting to think that the regex needs to be adjusted to suit each environment. Anyway by way of explanation here is what we did. Our systems are all placed in our nagios instance using the FQDN for the host name. These host names involve using characters such as - and . as well as numbers and letters.
From looking at the httpd logs on the sever I knew that there was a carriage return being inserted into the URL string and this is why the acknowledgement command wasn't working, so I figured I needed a way to strip out the carriage return from the URL string. So I started to look at the regex in the sysconfig (SystemMonitoring -> Core::PostMaster). Since posting to the list initially I had come across the following site
http://www.dippelschisser.de/2011/12/24/otrs-systemmonitoring-modul-zur-anbindung-von-nagios/ which seemed to have the same issue. Running it through google translate gave me a rough solution to amend the regex expression. This pointed me in the right direction, the change recommended on the site didn't work for me thanks to the characters we use in fqdns. So I used
http://www.regexpal.com/ to come up with a regex which would be able to pull the hostname from the nagios alert ticket without the trailing characters.
The result is a working acknowledgement in the nagios tickets, I am not sure if you would put this down as a fix, a hack or something else but whatever you want to call it we have it working for our environment. We ended up with a regex of \s*Host:\s+([\w-\. \* \\\. \* \\]*)\s* - Please keep in mind when looking at the regex I am no programmer! As a bonus we also got the CI status updateworking in the CMDB, turns out it was also having the trailing space issue.