Just a quick update on my problem. I've finally got it sorted and the problem isn't where I expected it to be.
I started to notice that I couldn't view multiple channels on the same transponder as well and after an error was experienced the TVServer couldn't preview any channels either until a restart of the service. So after getting totally pissed off I decided to downgrade to an older version of TVE3 which I knew worked. Only problem was the TV Plugin didn't seem to work at all with the new client. So I downgraded the client to 0.2.3 final with no SVNs and still no go for the plugin. So then I upgraded TVE3 to the version I was having trouble with and all was fine. EPG updates while timeshifting started to work and so did viewing multiple channels on the same transponder.
So it looks to me like something is happening in the client which is causing the TVService to have a little mental.
On the plus side all is now working for me, now on TVE3 rev 16587 but running 0.2.3 final without any SVNs for the client.
Hopefully this helps others out there and helps to track down this annoying one.