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I can add a few things here, and I'm having the same problem.  The plugin is officially titled ".html on PAGES", which adds .html to WordPress "Pages" using wp_rewrite.  The WordPress permalink structure does not affect "Pages", only "Posts".

What happens is the page the forum is placed on is accessible, but any subpages generated by SPF are not.  In the SPF Administration panel, the "current permalink" has the form "domain.com/forumpage.html" and SPF uses this permalink structure to write the links, such that forum links are in the form "domain.com/forumspage.html/forumtitle", where forumtitle is the name of one of the forums in a forum group.  However, SPF does not handle that link and we get a 404 error.  A little trial and error shows that the forum is accessible by taking the ".html" out of the link, so manually entering "domain.com/forumspage/forumtitle" displays the forum properly.

Now I'm not sure if this would work, but this is what I would like to try to do. Instead of letting SPF decide what the permalink structure is, I want to specify it as "domain.com/forumspage", without the .html.  Since there is no way to directly edit it in the SPF Administration panel, I tried manually setting it in the database, but SPF keeps resetting it.  So my question to you is, where is the php code that sets this option in the database?  I want to comment that code out so it doesn't execute. Then I will change the setting in the database and I believe it will work.

But (thinking outloud here (and following up I think I've confirmed it)), my thoughts are WordPress will still send you to the "forumpage.html", while SPF links all point to "forumpage/" followed by where ever you are going to, which it apparently recognizes since it still works.  Given that, I forsee a problem with SPF links that point back to the forums frontpage (forumpage/), which I do not think WordPress or SPF will not recognize, since it doesn't recognize it now.  I think another redirect would fix that.

I know this is a poor solution, but it's the only solution I can think of that might allow both plugins to work. Maybe a future SPF update could allow directly editing the "current permalink" and provide the redirect for it if a custom structure is used (or maybe there is an easier way).  I also posted on the .html-on-pages author's blog about adding a feature to exclude certain pages, which I think is the best solution.

Ok I'm done talking now, lol, I have been writing and trying things and double checking things for over an hour now.