This does not sound like an Application Modeller issue, rather behavior of the application itself and discovering how best to interface with it.
With any new application I interface with the first thing I do is perform an Application Assessment. This is basically a look at all the main elements in the appliction (buttons, combo boxes, grids, edit boxes etc) to evaluate the best way to interface with it. This feeds into the IPA's I create to estimate work, and informing all developers of the best way to interface with the appliction.
It is common to need to use the AA interface to interact with some HTML elements (if you have not already looked at the Browser Automation Guide on the portal (Methodology/Process Delivery Methodology (Reference Material)/Guides (Developer Reference Material)) I recommend you do.
It is also occassionally neccessary to use Global Mouse Clicks and Send Keys for bespoke non-standard elements. Where these are used it is neccessary to use an activate navigate stage with a tiny wait after it before you do any global clicks or send keys.
I hope this helps,
Den