Please help with how a filechooser works on a webpage

I must say that I have no idea about Java.
I am dealing with a webpage that has a "browse" button to add a file. The page seems to initiate java as java appears in my system tray when navigating to the page.
I have coming to this page through a totally different programming language and need to deal with the windows dialog (filechooser) that appears after clicking the "browse" button.
The thing is that after clicking the browse button - my code is stopped and only starts again after this dialog is closed.
So is it possible that the coder of this webpage has got his java (i think applet) so that once the dialog is open that no code can be run on the computer till the dialog is closed.

Ok thank you for your help. You have saved me a lot of time with my strange question.
I am sadely back in the darkages as I am using VBA which does not allow me to choose threads.
To make this question complete I am trying to automate an intranet web page. Of course there is an add file text box TYPE=File which is the cause of the problem. You cannot fill the box with something other than with SendKeys. (which only sometimes works).
So I wanted to "click" on the browse button and then my code should get a handle on the now open dialog, but my code is paused until the dialog is closed and it appears that java is doing this.
I assume it must be some security thing, maybe to stop exactly what I am doing. The funny thing is that the dialog is only model for the browser and my code. I can still do everything else with my computer. (I suppose the "everything else" is using another thread like you suggested.

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