You are correct that sometimes things made in layouts don't render the way you want on the web... and it can vary more significantly from browser to browser. WebDirect still is a 1.0 product and I expect some of these things will improve over time, but you are correct that some things do not render correctly and you have to play around with them in FileMaker layouts and test them in various web browsers to make sure they are displaying the way you want them to. Alternatively you can make your own PHP page and use Custom Web Publishing. But it is easier to just tweak things, albeit imperfectly, in layout mode than create all of that PHP code.
There is no specific application issue threat for developers. But you can post here in the general forums or there is one for Security and Servers. Most everything is available to everyone on Technet, so you aren't missing anything by looking here. This is a much flatter and less sectionalized discussion board than say FMForums. So ask away right here!
PS: Your left side is FMPA and right side of picture is web direct.
Is there now way to sort this ? I also have same issues with web direct .... colours and alignnment of text seem to change
I would say the issue is with your theme, you use a ton of elements that are sketchy for translation to CSS (gradients, shadows, rounded edges, overlapping objects, etc..)
The rendering engine for WebDirect is entirely different than the one in FileMaker. If you think about it, the browser is out of FileMaker's control, so there's no way to establish or guarantee a standard based on the rendering in FileMaker. FileMaker is sending the instructions blindly to the user, and counting on the browser to render those instructions. That makes any comparison for "this is what it looks like in FMP vs. WD" a moot point, and also explains why each WebDirect user can get a different looking layout. This is an easy tradeoff to swallow though, given that you're not writing a single line of HTML or CSS for your interface. FileMaker does a ton of work for you.
The best advice for people building WebDirect is to keep a separate set of layouts specifically for your WebDirect users (targeted interface development), or to develop for WebDirect, and not the desktop (lowest common denominator development).
If I was you, I would try and make the design flat, by removing gradient fills, shadows, and most curved edges. Better yet, I would just use the "tranquil" theme in filemaker, as it's close in look, but already optimized for use in WebDirect.