Jmicron sATA2 controller jm366 - BIOS update problems

I have a PCI-E sATA2 controller (http://www.jmicron.com/Product_JMB366.htm , http://www.startech.com/item-appli [...] Card.aspx) running on the PCI-E x4 slot on an Asus A8N-SLi Premium. I have been having problems trying to install XFX GT8800 SLi (http://www.tomshardware.co.uk/forum/page-259624_12_0.html#t1822470) and this card is the culprit - remove it & everything works fine - leave it in and the pc won't even POST.

There are 2 newer BIOS versions than the one I have installed (1.06.51) on the site (1.07.00 & 1.06.79) and a tool to update them (DOS flash utility) but when I run it it won't recognise the FLASH ROM but will recognise & backup the EEPROM. The backed up EEPROM file is 8kb, the bin file is 32kb. Sadly the documentation on the jmicron site is quite poor . . .

Q1 - do I need to update the EEPROM in order to then do the flash. If so is it the same bin file I use.
Q2 - is there some other problem??

thanks - MarkT