HTML5 output

Hi there

I have created a large set of templates using Storyline and have simplified them as much as possible but the HTML5 output is still incredibly poor. A lot of problems seem to be when layers are used, sometimes they show up and sometimes they don't. It's very hard to isolate what the problem is as the issues seem to be sporadic. A lot of the time the whole course just starts flashing for no obvious reason. The other issues seem to be related to using variables - it seems sometimes they get forgotten. 

From what I can tell I haven't included anything that Articulate doesn't say is supported here: http://www.articulate.com/support/kb_article.php?product=st1&id=1568gg1ayot2 but perhaps I've missed a trick! 

I don't want to use the player app as it does not track. This is unfortunate as the templates look great in that! 

Has any one else had issues such as these and what have they done to resolve them?

Thanks in advance,

Sally