ok i have found out some problems and some fixes and its all down to the following !
your Phisical BWA builder in the latest build is great
but the writeing methods in the latest version sucks
BW v4.2.5 is great !
now if you can impute the bwa version from the latest BW into v4.2.5 setup
then i think you have a winner !
read my post here you will see what i mean !..
i think this will solve a lot a problems with outher users aswell
this new emulation system you placed into the latest build is incredably crap hehe sorry to say it but it is…
i think your on with a winner if you put the latest version BWA builder into the 425 build and change the build number to above the latest version ! and i insist you say something about it in the updated log/ so people will know like me that you did what i sead and we should see posative responces at the mo im sticking with the above …
hope this helps mate…