Sorry forgot to mention i'm shooting DNG while bracketing (tried 3 and 5 images). I've had a quick try of the Romlog.lua included in the CHDK but it doesn't work and shows an error message.
You need to build CHDK with native calls enabled to use this. I believe the CHDKDE autobuilds have this enabled by default now: http://forum.chdk-treff.de/download.php
The save time doesn't seem to be the issue as the first 2 DNG shots appear save pretty quick with the 16GB Transcend card (quicker than the 4GB cards) however it just switches off when the 3rd shot has been taken. It does the same with the Toshiba 4GB card BUT NOT with the SanDisk Extreme 4GB. I thought the speed rating of the cards might have been causing the problem but unfortunately the 16GB (10) card doesn't work while the 4GB (6) card does, strange. The 16GB card will take bracketed jpgs no problem but not DNG.
Thanks for your help so far.
Save time is almost certainly the issue, as far as CHDK is concerned there is no other difference between cards.
Do you have raw buffer chached enabled ? If not turn it on. If you already have that on, you can try shooting CHDK raw instead. It saves quite a bit faster. You may have trouble converting CHDK raw to something useful, so be sure you can actually use the resulting files before you use it for anything other than testing.