I thought I'd devote an evening doing some more trouble shooting on this and I found the problem is definitely on my end, absolutely not a PWE / Cryptic server side issue. Finding this out was so elementary I could kick myself for not trying it before I even made this into an issue.
You see in the end I just pulled out another computer, dusted it off, copied my install directory across on a spare USB hard drive and STO ran perfectly first attempt Didn't even need to update it. Since everything else I run works perfectly on both systems, I can only assume there is a peculiarity I have yet to lock down on "this" computer. Something that strictly affects the Cryptic launcher and / or associated game executables yet no other software. I managed to replicate this issue using Champions Online: FFA but the PWE Forsaken World client worked fine on both systems without any issues. No issues running any other software either, just STO and Champions.
Both systems are running up to date versions of Avira Internet Security 2012, Windows 7 64, etc. If I can identify the cause of this issue I'll make another post in case it affects some other people too.